Starting phenix.real_space_refine on Tue Feb 11 15:36:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gyw_34378/02_2025/8gyw_34378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyw_34378/02_2025/8gyw_34378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gyw_34378/02_2025/8gyw_34378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyw_34378/02_2025/8gyw_34378.map" model { file = "/net/cci-nas-00/data/ceres_data/8gyw_34378/02_2025/8gyw_34378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyw_34378/02_2025/8gyw_34378.cif" } resolution = 3.9 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= 0.005 sd= 0.102 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 4 5.21 5 S 48 5.16 5 C 3994 2.51 5 N 984 2.21 5 O 1042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6076 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3005 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'CDC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 5.06, per 1000 atoms: 0.83 Number of scatterers: 6076 At special positions: 0 Unit cell: (97.37, 101.65, 71.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 4 15.00 Mg 4 11.99 O 1042 8.00 N 984 7.00 C 3994 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: 1.57 Conformation dependent library (CDL) restraints added in 641.0 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 80.7% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'B' and resid 28 through 37 Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 64 through 79 removed outlier: 3.539A pdb=" N MET B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 107 removed outlier: 3.756A pdb=" N ILE B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 143 removed outlier: 3.904A pdb=" N TYR B 119 " --> pdb=" O PRO B 115 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 173 removed outlier: 3.583A pdb=" N LEU B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 removed outlier: 3.663A pdb=" N THR B 177 " --> pdb=" O GLN B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 177' Processing helix chain 'B' and resid 178 through 204 Processing helix chain 'B' and resid 212 through 237 Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 247 through 272 removed outlier: 4.189A pdb=" N ALA B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 307 removed outlier: 3.883A pdb=" N LEU B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 315 through 341 Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 368 through 400 Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.539A pdb=" N MET A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 removed outlier: 3.756A pdb=" N ILE A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 143 removed outlier: 3.904A pdb=" N TYR A 119 " --> pdb=" O PRO A 115 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 173 removed outlier: 3.583A pdb=" N LEU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 removed outlier: 3.663A pdb=" N THR A 177 " --> pdb=" O GLN A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 178 through 204 Processing helix chain 'A' and resid 212 through 237 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 247 through 272 removed outlier: 4.190A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 287 through 307 removed outlier: 3.883A pdb=" N LEU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 315 through 341 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 351 through 363 Processing helix chain 'A' and resid 368 through 400 Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'B' and resid 238 through 239 removed outlier: 3.703A pdb=" N ILE B 239 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE B 244 " --> pdb=" O ILE B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.703A pdb=" N ILE A 239 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 244 " --> pdb=" O ILE A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 441 hydrogen bonds defined for protein. 1311 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: 1.77 Time building geometry restraints manager: 1.82 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: 1379 1.34 - 1.45: 1411 1.45 - 1.57: 3380 1.57 - 1.69: 12 1.69 - 1.81: 66 Bond restraints: 6248 Sorted by residual: bond pdb=" CB PRO A 115 " pdb=" CG PRO A 115 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.56e+00 bond pdb=" CB PRO B 115 " pdb=" CG PRO B 115 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.55e+00 bond pdb=" CA PRO A 108 " pdb=" C PRO A 108 " ideal model delta sigma weight residual 1.517 1.559 -0.042 1.54e-02 4.22e+03 7.49e+00 bond pdb=" CA PRO B 108 " pdb=" C PRO B 108 " ideal model delta sigma weight residual 1.517 1.558 -0.042 1.54e-02 4.22e+03 7.39e+00 bond pdb=" CB PRO B 108 " pdb=" CG PRO B 108 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.74e+00 ... (remaining 6243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 8287 3.79 - 7.58: 197 7.58 - 11.38: 26 11.38 - 15.17: 12 15.17 - 18.96: 2 Bond angle restraints: 8524 Sorted by residual: angle pdb=" CA PRO A 115 " pdb=" N PRO A 115 " pdb=" CD PRO A 115 " ideal model delta sigma weight residual 112.00 99.70 12.30 1.40e+00 5.10e-01 7.72e+01 angle pdb=" CA PRO B 115 " pdb=" N PRO B 115 " pdb=" CD PRO B 115 " ideal model delta sigma weight residual 112.00 99.71 12.29 1.40e+00 5.10e-01 7.71e+01 angle pdb=" CA PRO A 108 " pdb=" N PRO A 108 " pdb=" CD PRO A 108 " ideal model delta sigma weight residual 112.00 100.26 11.74 1.40e+00 5.10e-01 7.03e+01 angle pdb=" CA PRO B 108 " pdb=" N PRO B 108 " pdb=" CD PRO B 108 " ideal model delta sigma weight residual 112.00 100.28 11.72 1.40e+00 5.10e-01 7.01e+01 angle pdb=" CA LEU A 48 " pdb=" CB LEU A 48 " pdb=" CG LEU A 48 " ideal model delta sigma weight residual 116.30 135.26 -18.96 3.50e+00 8.16e-02 2.93e+01 ... (remaining 8519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 3182 16.52 - 33.04: 286 33.04 - 49.56: 98 49.56 - 66.08: 54 66.08 - 82.61: 14 Dihedral angle restraints: 3634 sinusoidal: 1426 harmonic: 2208 Sorted by residual: dihedral pdb=" C PRO B 108 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " pdb=" CB PRO B 108 " ideal model delta harmonic sigma weight residual -120.70 -129.60 8.90 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" C PRO A 108 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " pdb=" CB PRO A 108 " ideal model delta harmonic sigma weight residual -120.70 -129.55 8.85 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" CA ASP A 348 " pdb=" CB ASP A 348 " pdb=" CG ASP A 348 " pdb=" OD1 ASP A 348 " ideal model delta sinusoidal sigma weight residual -30.00 -89.32 59.32 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 3631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 758 0.081 - 0.162: 188 0.162 - 0.244: 30 0.244 - 0.325: 6 0.325 - 0.406: 2 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA PRO B 108 " pdb=" N PRO B 108 " pdb=" C PRO B 108 " pdb=" CB PRO B 108 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA PRO A 108 " pdb=" N PRO A 108 " pdb=" C PRO A 108 " pdb=" CB PRO A 108 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB THR A 214 " pdb=" CA THR A 214 " pdb=" OG1 THR A 214 " pdb=" CG2 THR A 214 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 981 not shown) Planarity restraints: 1036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 114 " 0.103 5.00e-02 4.00e+02 1.45e-01 3.39e+01 pdb=" N PRO A 115 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 114 " 0.102 5.00e-02 4.00e+02 1.45e-01 3.37e+01 pdb=" N PRO B 115 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 107 " -0.094 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO A 108 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.071 5.00e-02 4.00e+02 ... (remaining 1033 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 38 2.59 - 3.17: 5029 3.17 - 3.74: 9890 3.74 - 4.32: 12054 4.32 - 4.90: 20504 Nonbonded interactions: 47515 Sorted by model distance: nonbonded pdb=" OD1 ASP B 154 " pdb="MG MG B 502 " model vdw 2.008 2.170 nonbonded pdb=" OD1 ASP A 154 " pdb="MG MG A 502 " model vdw 2.009 2.170 nonbonded pdb="MG MG B 502 " pdb=" O2B CDC B 503 " model vdw 2.085 2.170 nonbonded pdb="MG MG A 502 " pdb=" O2B CDC A 503 " model vdw 2.086 2.170 nonbonded pdb=" OD1 ASP A 180 " pdb=" OH TYR A 304 " model vdw 2.269 3.040 ... (remaining 47510 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 0.550 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.690 Find NCS groups from input model: 0.120 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.008 0.146 6248 Z= 0.534 Angle : 1.459 18.960 8524 Z= 0.833 Chirality : 0.077 0.406 984 Planarity : 0.015 0.199 1036 Dihedral : 16.780 82.606 2210 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.30 % Allowed : 19.94 % Favored : 79.76 % 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: 1.24 (0.29), residues: 756 helix: 0.99 (0.20), residues: 554 sheet: None (None), residues: 0 loop : 0.67 (0.47), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP B 181 HIS 0.007 0.002 HIS A 46 PHE 0.069 0.004 PHE B 234 TYR 0.047 0.006 TYR A 362 ARG 0.010 0.002 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLN cc_start: 0.8807 (mt0) cc_final: 0.8524 (mt0) REVERT: B 82 TRP cc_start: 0.8514 (p90) cc_final: 0.8297 (p90) REVERT: B 130 GLN cc_start: 0.8216 (tp40) cc_final: 0.7863 (tp-100) REVERT: B 344 MET cc_start: 0.7872 (mtp) cc_final: 0.7572 (mtt) REVERT: B 361 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8108 (mm-40) REVERT: A 82 TRP cc_start: 0.8500 (p90) cc_final: 0.8279 (p90) REVERT: A 130 GLN cc_start: 0.8265 (tp40) cc_final: 0.7914 (tp-100) REVERT: A 361 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8294 (mm-40) outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.2049 time to fit residues: 49.8783 Evaluate side-chains 172 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.184061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143738 restraints weight = 7854.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.148855 restraints weight = 4384.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.152367 restraints weight = 2972.076| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6248 Z= 0.196 Angle : 0.631 8.728 8524 Z= 0.330 Chirality : 0.042 0.132 984 Planarity : 0.005 0.051 1036 Dihedral : 7.521 52.373 874 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 4.08 % Allowed : 16.47 % Favored : 79.46 % 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: 2.74 (0.29), residues: 756 helix: 2.16 (0.20), residues: 558 sheet: None (None), residues: 0 loop : 0.99 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 117 HIS 0.004 0.001 HIS B 315 PHE 0.017 0.002 PHE B 358 TYR 0.012 0.002 TYR B 387 ARG 0.007 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8531 (mmm) REVERT: B 142 ARG cc_start: 0.8101 (tpt90) cc_final: 0.7768 (tpt90) REVERT: B 260 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8198 (t80) REVERT: A 142 ARG cc_start: 0.8192 (tpt90) cc_final: 0.7821 (tpt90) REVERT: A 260 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8213 (t80) REVERT: A 302 MET cc_start: 0.8752 (mmm) cc_final: 0.8545 (mmt) outliers start: 27 outliers final: 16 residues processed: 191 average time/residue: 0.2004 time to fit residues: 48.5874 Evaluate side-chains 175 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN A 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.179013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137539 restraints weight = 8030.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142405 restraints weight = 4591.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.145648 restraints weight = 3181.212| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6248 Z= 0.224 Angle : 0.590 6.080 8524 Z= 0.309 Chirality : 0.042 0.147 984 Planarity : 0.004 0.036 1036 Dihedral : 6.036 44.990 874 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 5.29 % Allowed : 18.43 % Favored : 76.28 % 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: 3.05 (0.30), residues: 756 helix: 2.35 (0.20), residues: 558 sheet: None (None), residues: 0 loop : 1.21 (0.51), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 117 HIS 0.004 0.001 HIS A 315 PHE 0.016 0.002 PHE A 187 TYR 0.010 0.002 TYR A 387 ARG 0.003 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 ARG cc_start: 0.8281 (tpt90) cc_final: 0.7983 (tpt90) REVERT: B 193 PHE cc_start: 0.8277 (t80) cc_final: 0.8043 (t80) REVERT: B 260 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8119 (t80) REVERT: B 306 LYS cc_start: 0.8161 (tppt) cc_final: 0.7950 (tppt) REVERT: A 260 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8080 (t80) REVERT: A 302 MET cc_start: 0.8777 (mmm) cc_final: 0.8277 (mtt) REVERT: A 306 LYS cc_start: 0.8101 (tppt) cc_final: 0.7861 (tppt) outliers start: 35 outliers final: 25 residues processed: 181 average time/residue: 0.1879 time to fit residues: 43.6640 Evaluate side-chains 188 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 69 GLN A 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.175082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.134436 restraints weight = 8203.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.139129 restraints weight = 4804.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.142367 restraints weight = 3358.482| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6248 Z= 0.215 Angle : 0.582 9.482 8524 Z= 0.302 Chirality : 0.042 0.146 984 Planarity : 0.004 0.038 1036 Dihedral : 5.832 43.919 874 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 5.59 % Allowed : 20.09 % Favored : 74.32 % 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: 2.99 (0.30), residues: 756 helix: 2.28 (0.20), residues: 558 sheet: None (None), residues: 0 loop : 1.29 (0.51), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 117 HIS 0.004 0.001 HIS B 197 PHE 0.022 0.002 PHE B 234 TYR 0.012 0.001 TYR A 387 ARG 0.004 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 ARG cc_start: 0.8162 (mpt-90) cc_final: 0.7729 (mmt-90) REVERT: B 174 GLN cc_start: 0.9121 (mt0) cc_final: 0.8693 (mt0) REVERT: B 260 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.7991 (t80) REVERT: A 55 ARG cc_start: 0.7768 (tpp80) cc_final: 0.7487 (mmt-90) REVERT: A 127 PHE cc_start: 0.8841 (t80) cc_final: 0.8612 (t80) REVERT: A 174 GLN cc_start: 0.9148 (mt0) cc_final: 0.8704 (mt0) REVERT: A 302 MET cc_start: 0.8854 (mmm) cc_final: 0.8359 (mtp) outliers start: 37 outliers final: 24 residues processed: 193 average time/residue: 0.2298 time to fit residues: 55.3941 Evaluate side-chains 195 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 41 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.175763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136300 restraints weight = 8242.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.141566 restraints weight = 4565.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145074 restraints weight = 3069.950| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6248 Z= 0.202 Angle : 0.622 10.946 8524 Z= 0.311 Chirality : 0.041 0.125 984 Planarity : 0.004 0.040 1036 Dihedral : 5.611 41.268 874 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.83 % Allowed : 23.87 % Favored : 71.30 % 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: 2.85 (0.30), residues: 756 helix: 2.23 (0.20), residues: 560 sheet: None (None), residues: 0 loop : 1.02 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 235 HIS 0.004 0.001 HIS B 197 PHE 0.014 0.001 PHE B 187 TYR 0.013 0.001 TYR B 362 ARG 0.006 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 ARG cc_start: 0.8342 (mmt90) cc_final: 0.8017 (mpt-90) REVERT: B 174 GLN cc_start: 0.9144 (mt0) cc_final: 0.8941 (mt0) REVERT: B 182 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8242 (ttp) REVERT: B 260 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7977 (t80) REVERT: B 306 LYS cc_start: 0.8034 (tppt) cc_final: 0.7761 (tppt) REVERT: B 367 ILE cc_start: 0.8326 (mm) cc_final: 0.8049 (tt) REVERT: A 127 PHE cc_start: 0.8859 (t80) cc_final: 0.8626 (t80) REVERT: A 182 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8255 (ttp) REVERT: A 260 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7975 (t80) REVERT: A 302 MET cc_start: 0.8796 (mmm) cc_final: 0.8408 (mtp) REVERT: A 367 ILE cc_start: 0.8316 (mm) cc_final: 0.8064 (tt) outliers start: 32 outliers final: 22 residues processed: 182 average time/residue: 0.2194 time to fit residues: 49.8964 Evaluate side-chains 187 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN A 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.173749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135054 restraints weight = 8265.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140112 restraints weight = 4596.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143662 restraints weight = 3107.258| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6248 Z= 0.219 Angle : 0.620 11.385 8524 Z= 0.313 Chirality : 0.042 0.129 984 Planarity : 0.004 0.042 1036 Dihedral : 5.463 39.062 874 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 5.89 % Allowed : 23.11 % Favored : 71.00 % 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: 2.95 (0.30), residues: 756 helix: 2.24 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 1.33 (0.50), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 235 HIS 0.004 0.001 HIS B 338 PHE 0.021 0.002 PHE A 234 TYR 0.018 0.002 TYR B 362 ARG 0.006 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.8787 (t80) cc_final: 0.8554 (t80) REVERT: B 182 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8284 (ttp) REVERT: B 260 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7968 (t80) REVERT: B 306 LYS cc_start: 0.8026 (tppt) cc_final: 0.7774 (tppt) REVERT: B 307 SER cc_start: 0.8983 (t) cc_final: 0.8710 (t) REVERT: A 127 PHE cc_start: 0.8872 (t80) cc_final: 0.8634 (t80) REVERT: A 182 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8311 (ttp) REVERT: A 260 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7945 (t80) REVERT: A 302 MET cc_start: 0.8756 (mmm) cc_final: 0.8451 (mtp) REVERT: A 307 SER cc_start: 0.9013 (t) cc_final: 0.8749 (t) outliers start: 39 outliers final: 29 residues processed: 187 average time/residue: 0.1941 time to fit residues: 46.4175 Evaluate side-chains 199 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 23 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 29 optimal weight: 0.4980 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.175398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136457 restraints weight = 8361.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.141741 restraints weight = 4692.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145285 restraints weight = 3173.284| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6248 Z= 0.210 Angle : 0.643 12.139 8524 Z= 0.320 Chirality : 0.041 0.129 984 Planarity : 0.004 0.041 1036 Dihedral : 5.493 38.502 874 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.98 % Allowed : 25.83 % Favored : 69.18 % 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: 2.80 (0.30), residues: 756 helix: 2.15 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 1.17 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 235 HIS 0.003 0.001 HIS A 315 PHE 0.015 0.001 PHE B 358 TYR 0.020 0.001 TYR A 362 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 ARG cc_start: 0.8557 (mmt90) cc_final: 0.8289 (mmt90) REVERT: B 182 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8242 (ttp) REVERT: B 260 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7921 (t80) REVERT: B 306 LYS cc_start: 0.7920 (tppt) cc_final: 0.7581 (tppt) REVERT: B 307 SER cc_start: 0.8989 (t) cc_final: 0.8712 (t) REVERT: A 127 PHE cc_start: 0.8946 (t80) cc_final: 0.8704 (t80) REVERT: A 182 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8273 (ttp) REVERT: A 246 MET cc_start: 0.8037 (tpp) cc_final: 0.7757 (tpp) REVERT: A 260 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8005 (t80) REVERT: A 302 MET cc_start: 0.8737 (mmm) cc_final: 0.8463 (mtp) REVERT: A 307 SER cc_start: 0.8989 (t) cc_final: 0.8721 (t) outliers start: 33 outliers final: 26 residues processed: 182 average time/residue: 0.2069 time to fit residues: 48.1514 Evaluate side-chains 197 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.176683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138318 restraints weight = 8223.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.143624 restraints weight = 4508.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147111 restraints weight = 3004.015| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6248 Z= 0.196 Angle : 0.629 11.994 8524 Z= 0.314 Chirality : 0.040 0.130 984 Planarity : 0.004 0.041 1036 Dihedral : 5.449 38.364 874 Min Nonbonded Distance : 1.517 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 5.14 % Allowed : 26.28 % Favored : 68.58 % 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: 2.77 (0.30), residues: 756 helix: 2.15 (0.21), residues: 562 sheet: None (None), residues: 0 loop : 1.08 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 117 HIS 0.003 0.001 HIS B 197 PHE 0.019 0.001 PHE A 234 TYR 0.017 0.001 TYR A 362 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 260 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7869 (t80) REVERT: B 306 LYS cc_start: 0.7756 (tppt) cc_final: 0.7474 (tppt) REVERT: B 307 SER cc_start: 0.8960 (t) cc_final: 0.8677 (t) REVERT: A 127 PHE cc_start: 0.8943 (t80) cc_final: 0.8685 (t80) REVERT: A 130 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7800 (tp-100) REVERT: A 182 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8300 (ttp) REVERT: A 260 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7924 (t80) REVERT: A 307 SER cc_start: 0.8953 (t) cc_final: 0.8682 (t) outliers start: 34 outliers final: 26 residues processed: 188 average time/residue: 0.1986 time to fit residues: 47.7471 Evaluate side-chains 192 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 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 = 0.3984 r_free = 0.3984 target = 0.172606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133588 restraints weight = 8401.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138875 restraints weight = 4667.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142478 restraints weight = 3135.657| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6248 Z= 0.247 Angle : 0.672 13.098 8524 Z= 0.336 Chirality : 0.042 0.144 984 Planarity : 0.005 0.041 1036 Dihedral : 5.368 36.519 874 Min Nonbonded Distance : 1.397 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 5.29 % Allowed : 25.68 % Favored : 69.03 % 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: 2.81 (0.30), residues: 756 helix: 2.14 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 1.23 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 117 HIS 0.004 0.001 HIS B 197 PHE 0.016 0.001 PHE A 358 TYR 0.015 0.001 TYR A 362 ARG 0.010 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 260 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7848 (t80) REVERT: B 306 LYS cc_start: 0.7813 (tppt) cc_final: 0.7525 (tppt) REVERT: A 98 CYS cc_start: 0.7608 (m) cc_final: 0.7305 (p) REVERT: A 127 PHE cc_start: 0.8932 (t80) cc_final: 0.8692 (t80) REVERT: A 182 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8357 (ttp) REVERT: A 260 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.7960 (t80) REVERT: A 307 SER cc_start: 0.9036 (t) cc_final: 0.8816 (t) outliers start: 35 outliers final: 29 residues processed: 180 average time/residue: 0.1852 time to fit residues: 43.0247 Evaluate side-chains 195 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 4 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.176219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137670 restraints weight = 8300.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143002 restraints weight = 4550.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146681 restraints weight = 3032.596| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6248 Z= 0.208 Angle : 0.657 13.151 8524 Z= 0.330 Chirality : 0.041 0.167 984 Planarity : 0.005 0.041 1036 Dihedral : 5.424 37.590 874 Min Nonbonded Distance : 1.327 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.98 % Allowed : 27.34 % Favored : 67.67 % 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 (0.30), residues: 756 helix: 2.03 (0.21), residues: 574 sheet: None (None), residues: 0 loop : 0.80 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 181 HIS 0.003 0.001 HIS B 197 PHE 0.023 0.001 PHE A 234 TYR 0.010 0.001 TYR B 119 ARG 0.010 0.000 ARG B 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 246 MET cc_start: 0.7622 (tpp) cc_final: 0.7073 (tpp) REVERT: B 260 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7897 (t80) REVERT: B 306 LYS cc_start: 0.7721 (tppt) cc_final: 0.7410 (tppt) REVERT: A 45 ARG cc_start: 0.7244 (ttt90) cc_final: 0.6921 (tmm160) REVERT: A 127 PHE cc_start: 0.8937 (t80) cc_final: 0.8700 (t80) REVERT: A 182 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8292 (ttp) REVERT: A 260 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7963 (t80) REVERT: A 307 SER cc_start: 0.9041 (t) cc_final: 0.8797 (t) outliers start: 33 outliers final: 29 residues processed: 179 average time/residue: 0.1888 time to fit residues: 43.0841 Evaluate side-chains 196 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 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 = 0.4035 r_free = 0.4035 target = 0.176925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138209 restraints weight = 8530.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143601 restraints weight = 4640.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147270 restraints weight = 3077.216| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6248 Z= 0.206 Angle : 0.656 13.278 8524 Z= 0.329 Chirality : 0.041 0.157 984 Planarity : 0.005 0.041 1036 Dihedral : 5.323 36.407 874 Min Nonbonded Distance : 1.273 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.98 % Allowed : 26.89 % Favored : 68.13 % 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 (0.29), residues: 756 helix: 2.10 (0.21), residues: 564 sheet: None (None), residues: 0 loop : 0.75 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 117 HIS 0.004 0.001 HIS B 197 PHE 0.016 0.001 PHE A 358 TYR 0.015 0.001 TYR A 362 ARG 0.010 0.000 ARG B 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2040.75 seconds wall clock time: 37 minutes 31.21 seconds (2251.21 seconds total)