Starting phenix.real_space_refine on Fri Dec 27 18:03:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gyx_34379/12_2024/8gyx_34379.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyx_34379/12_2024/8gyx_34379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gyx_34379/12_2024/8gyx_34379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyx_34379/12_2024/8gyx_34379.map" model { file = "/net/cci-nas-00/data/ceres_data/8gyx_34379/12_2024/8gyx_34379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyx_34379/12_2024/8gyx_34379.cif" } resolution = 3.7 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= 0.004 sd= 0.108 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 2 5.49 5 Mg 4 5.21 5 S 48 5.16 5 C 4050 2.51 5 N 978 2.21 5 O 1036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6118 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 5.27, per 1000 atoms: 0.86 Number of scatterers: 6118 At special positions: 0 Unit cell: (108.07, 90.95, 72.76, 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 2 15.00 Mg 4 11.99 O 1036 8.00 N 978 7.00 C 4050 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: 1.64 Conformation dependent library (CDL) restraints added in 750.1 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: 36 helices and 0 sheets defined 80.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'B' and resid 28 through 36 Processing helix chain 'B' and resid 44 through 53 removed outlier: 3.808A pdb=" N GLU B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 79 removed outlier: 3.966A pdb=" N GLY B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 107 Processing helix chain 'B' and resid 115 through 143 removed outlier: 3.922A pdb=" N TYR B 119 " --> pdb=" O PRO B 115 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 174 removed outlier: 3.595A pdb=" N LEU B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 178 through 204 Processing helix chain 'B' and resid 212 through 237 removed outlier: 3.540A pdb=" N LEU B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 248 through 272 removed outlier: 3.702A 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: 3.884A pdb=" N LEU B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N HIS B 292 " --> pdb=" O SER B 288 " (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 36 Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.808A pdb=" N GLU A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.967A pdb=" N GLY A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'A' and resid 115 through 143 removed outlier: 3.922A pdb=" N TYR A 119 " --> pdb=" O PRO A 115 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 174 removed outlier: 3.596A pdb=" N LEU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 204 Processing helix chain 'A' and resid 212 through 237 removed outlier: 3.540A pdb=" N LEU A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 248 through 272 removed outlier: 3.703A 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: 3.885A pdb=" N LEU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N HIS A 292 " --> pdb=" O SER A 288 " (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 400 439 hydrogen bonds defined for protein. 1305 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: 1.71 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 898 1.32 - 1.44: 1812 1.44 - 1.57: 3498 1.57 - 1.69: 12 1.69 - 1.81: 66 Bond restraints: 6286 Sorted by residual: bond pdb=" O12 POV A 501 " pdb=" P POV A 501 " ideal model delta sigma weight residual 1.657 1.601 0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" O12 POV B 501 " pdb=" P POV B 501 " ideal model delta sigma weight residual 1.657 1.601 0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" CB ASN B 144 " pdb=" CG ASN B 144 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.50e-02 1.60e+03 5.80e+00 bond pdb=" CB ASN A 144 " pdb=" CG ASN A 144 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.50e-02 1.60e+03 5.77e+00 bond pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " ideal model delta sigma weight residual 1.529 1.567 -0.038 1.62e-02 3.81e+03 5.49e+00 ... (remaining 6281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 8317 3.64 - 7.27: 197 7.27 - 10.91: 22 10.91 - 14.54: 4 14.54 - 18.18: 4 Bond angle restraints: 8544 Sorted by residual: angle pdb=" CB MET A 339 " pdb=" CG MET A 339 " pdb=" SD MET A 339 " ideal model delta sigma weight residual 112.70 130.88 -18.18 3.00e+00 1.11e-01 3.67e+01 angle pdb=" CB MET B 339 " pdb=" CG MET B 339 " pdb=" SD MET B 339 " ideal model delta sigma weight residual 112.70 130.87 -18.17 3.00e+00 1.11e-01 3.67e+01 angle pdb=" CA PRO B 148 " pdb=" N PRO B 148 " pdb=" CD PRO B 148 " ideal model delta sigma weight residual 112.00 104.61 7.39 1.40e+00 5.10e-01 2.79e+01 angle pdb=" CA PRO A 148 " pdb=" N PRO A 148 " pdb=" CD PRO A 148 " ideal model delta sigma weight residual 112.00 104.64 7.36 1.40e+00 5.10e-01 2.76e+01 angle pdb=" CA ASN B 144 " pdb=" CB ASN B 144 " pdb=" CG ASN B 144 " ideal model delta sigma weight residual 112.60 117.61 -5.01 1.00e+00 1.00e+00 2.51e+01 ... (remaining 8539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 3233 18.09 - 36.17: 305 36.17 - 54.26: 90 54.26 - 72.34: 20 72.34 - 90.43: 6 Dihedral angle restraints: 3654 sinusoidal: 1446 harmonic: 2208 Sorted by residual: dihedral pdb=" C ASN B 144 " pdb=" N ASN B 144 " pdb=" CA ASN B 144 " pdb=" CB ASN B 144 " ideal model delta harmonic sigma weight residual -122.60 -131.96 9.36 0 2.50e+00 1.60e-01 1.40e+01 dihedral pdb=" C ASN A 144 " pdb=" N ASN A 144 " pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" CA ASP B 348 " pdb=" CB ASP B 348 " pdb=" CG ASP B 348 " pdb=" OD1 ASP B 348 " ideal model delta sinusoidal sigma weight residual -30.00 -89.29 59.29 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 3651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 796 0.082 - 0.164: 142 0.164 - 0.245: 34 0.245 - 0.327: 2 0.327 - 0.409: 4 Chirality restraints: 978 Sorted by residual: chirality pdb=" CB ILE A 222 " pdb=" CA ILE A 222 " pdb=" CG1 ILE A 222 " pdb=" CG2 ILE A 222 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CB ILE B 222 " pdb=" CA ILE B 222 " pdb=" CG1 ILE B 222 " pdb=" CG2 ILE B 222 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA PRO A 148 " pdb=" N PRO A 148 " pdb=" C PRO A 148 " pdb=" CB PRO A 148 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 975 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 501 " -0.096 2.00e-02 2.50e+03 2.38e-01 5.67e+02 pdb=" C29 POV B 501 " 0.317 2.00e-02 2.50e+03 pdb="C210 POV B 501 " -0.325 2.00e-02 2.50e+03 pdb="C211 POV B 501 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 501 " 0.096 2.00e-02 2.50e+03 2.38e-01 5.66e+02 pdb=" C29 POV A 501 " -0.317 2.00e-02 2.50e+03 pdb="C210 POV A 501 " 0.325 2.00e-02 2.50e+03 pdb="C211 POV A 501 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 147 " -0.071 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO A 148 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 148 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 148 " -0.057 5.00e-02 4.00e+02 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 316 2.75 - 3.28: 6486 3.28 - 3.82: 10094 3.82 - 4.36: 11692 4.36 - 4.90: 20113 Nonbonded interactions: 48701 Sorted by model distance: nonbonded pdb=" OD1 ASP A 133 " pdb="MG MG A 502 " model vdw 2.208 2.170 nonbonded pdb=" OD1 ASP B 133 " pdb="MG MG B 502 " model vdw 2.208 2.170 nonbonded pdb=" OD2 ASP B 158 " pdb="MG MG B 503 " model vdw 2.234 2.170 nonbonded pdb=" OD2 ASP A 158 " pdb="MG MG A 503 " model vdw 2.235 2.170 nonbonded pdb=" OG1 THR A 143 " pdb=" OG SER A 145 " model vdw 2.261 3.040 ... (remaining 48696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.430 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.270 Find NCS groups from input model: 0.160 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 6286 Z= 0.447 Angle : 1.358 18.179 8544 Z= 0.780 Chirality : 0.072 0.409 978 Planarity : 0.014 0.238 1040 Dihedral : 16.071 90.426 2230 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.30 % Allowed : 19.64 % Favored : 80.06 % 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: 1.06 (0.28), residues: 756 helix: 0.85 (0.20), residues: 548 sheet: None (None), residues: 0 loop : 0.67 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 74 HIS 0.031 0.004 HIS A 46 PHE 0.056 0.003 PHE B 260 TYR 0.046 0.005 TYR B 387 ARG 0.014 0.003 ARG A 50 *********************** 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 165 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 0.697 Fit side-chains REVERT: B 131 SER cc_start: 0.8853 (m) cc_final: 0.8614 (m) REVERT: B 267 ARG cc_start: 0.7786 (ptm160) cc_final: 0.7433 (ptm160) REVERT: A 131 SER cc_start: 0.8866 (m) cc_final: 0.8658 (m) outliers start: 2 outliers final: 2 residues processed: 164 average time/residue: 0.2108 time to fit residues: 44.0181 Evaluate side-chains 160 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain A residue 149 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 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 130 GLN B 197 HIS ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN A 57 GLN A 130 GLN A 197 HIS ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6286 Z= 0.218 Angle : 0.642 10.180 8544 Z= 0.335 Chirality : 0.043 0.151 978 Planarity : 0.005 0.061 1040 Dihedral : 10.963 87.806 898 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 3.78 % Allowed : 18.13 % Favored : 78.10 % 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: 2.66 (0.29), residues: 756 helix: 2.10 (0.20), residues: 570 sheet: None (None), residues: 0 loop : 0.84 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 74 HIS 0.006 0.001 HIS B 46 PHE 0.019 0.002 PHE A 358 TYR 0.015 0.002 TYR A 362 ARG 0.005 0.001 ARG B 50 *********************** 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 218 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: B 69 GLN cc_start: 0.8632 (tp40) cc_final: 0.8413 (tp40) REVERT: B 219 PHE cc_start: 0.7431 (t80) cc_final: 0.6927 (m-10) REVERT: B 267 ARG cc_start: 0.8014 (ptm160) cc_final: 0.7642 (ptm160) REVERT: B 347 HIS cc_start: 0.8140 (p90) cc_final: 0.7567 (p90) REVERT: B 360 ASP cc_start: 0.9032 (t70) cc_final: 0.8643 (t0) REVERT: B 362 TYR cc_start: 0.9047 (t80) cc_final: 0.8582 (t80) REVERT: A 50 ARG cc_start: 0.7830 (ttm110) cc_final: 0.7597 (ttp-110) REVERT: A 69 GLN cc_start: 0.8611 (tp40) cc_final: 0.8391 (tp40) REVERT: A 119 TYR cc_start: 0.8779 (m-10) cc_final: 0.8436 (m-10) REVERT: A 219 PHE cc_start: 0.7454 (t80) cc_final: 0.6923 (m-10) REVERT: A 347 HIS cc_start: 0.8157 (p90) cc_final: 0.7366 (p-80) REVERT: A 360 ASP cc_start: 0.9050 (t70) cc_final: 0.8678 (t0) REVERT: A 362 TYR cc_start: 0.9048 (t80) cc_final: 0.8603 (t80) outliers start: 25 outliers final: 19 residues processed: 209 average time/residue: 0.1987 time to fit residues: 52.8782 Evaluate side-chains 205 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 365 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 57 GLN B 217 GLN B 224 HIS A 217 GLN A 224 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 6286 Z= 0.313 Angle : 0.638 8.249 8544 Z= 0.339 Chirality : 0.045 0.146 978 Planarity : 0.005 0.049 1040 Dihedral : 10.717 83.171 898 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 5.89 % Allowed : 20.69 % Favored : 73.41 % 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: 2.55 (0.29), residues: 756 helix: 2.07 (0.20), residues: 570 sheet: None (None), residues: 0 loop : 0.63 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 181 HIS 0.005 0.001 HIS A 315 PHE 0.023 0.002 PHE B 234 TYR 0.017 0.002 TYR A 201 ARG 0.002 0.000 ARG B 50 *********************** 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 258 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.750 Fit side-chains REVERT: B 69 GLN cc_start: 0.8560 (tp40) cc_final: 0.8349 (tp40) REVERT: B 78 ARG cc_start: 0.8639 (mmm160) cc_final: 0.8090 (mmm-85) REVERT: B 119 TYR cc_start: 0.8866 (m-10) cc_final: 0.8611 (m-10) REVERT: B 199 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8417 (tm-30) REVERT: B 252 LEU cc_start: 0.8896 (mt) cc_final: 0.8614 (mt) REVERT: B 329 LYS cc_start: 0.8029 (tttp) cc_final: 0.7812 (tttm) REVERT: B 360 ASP cc_start: 0.8824 (t70) cc_final: 0.8381 (t0) REVERT: B 362 TYR cc_start: 0.9106 (t80) cc_final: 0.8759 (t80) REVERT: B 387 TYR cc_start: 0.8449 (t80) cc_final: 0.8233 (t80) REVERT: A 69 GLN cc_start: 0.8567 (tp40) cc_final: 0.8366 (tp40) REVERT: A 74 TRP cc_start: 0.8052 (t60) cc_final: 0.7850 (t60) REVERT: A 119 TYR cc_start: 0.8876 (m-10) cc_final: 0.8628 (m-10) REVERT: A 252 LEU cc_start: 0.8903 (mt) cc_final: 0.8610 (mt) REVERT: A 329 LYS cc_start: 0.8015 (tttp) cc_final: 0.7805 (tttm) REVERT: A 360 ASP cc_start: 0.8839 (t70) cc_final: 0.8403 (t0) REVERT: A 362 TYR cc_start: 0.9113 (t80) cc_final: 0.8779 (t80) outliers start: 39 outliers final: 33 residues processed: 238 average time/residue: 0.1991 time to fit residues: 60.4085 Evaluate side-chains 232 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 385 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 HIS ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 HIS A 46 HIS A 224 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6286 Z= 0.193 Angle : 0.582 9.340 8544 Z= 0.306 Chirality : 0.041 0.156 978 Planarity : 0.005 0.042 1040 Dihedral : 10.171 80.105 898 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.93 % Allowed : 26.13 % Favored : 69.94 % 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: 2.58 (0.30), residues: 756 helix: 2.11 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 0.51 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 117 HIS 0.004 0.001 HIS B 46 PHE 0.015 0.001 PHE A 187 TYR 0.016 0.001 TYR B 201 ARG 0.006 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 212 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.621 Fit side-chains REVERT: B 69 GLN cc_start: 0.8453 (tp40) cc_final: 0.8190 (tp40) REVERT: B 119 TYR cc_start: 0.8858 (m-10) cc_final: 0.8612 (m-10) REVERT: B 149 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8725 (tt) REVERT: B 252 LEU cc_start: 0.8871 (mt) cc_final: 0.8579 (mt) REVERT: B 305 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8734 (mmmt) REVERT: B 360 ASP cc_start: 0.8799 (t70) cc_final: 0.8339 (t0) REVERT: B 362 TYR cc_start: 0.9075 (t80) cc_final: 0.8676 (t80) REVERT: B 381 PHE cc_start: 0.8363 (t80) cc_final: 0.7872 (t80) REVERT: A 69 GLN cc_start: 0.8531 (tp40) cc_final: 0.8295 (tp40) REVERT: A 74 TRP cc_start: 0.7973 (t60) cc_final: 0.7745 (t60) REVERT: A 119 TYR cc_start: 0.8836 (m-10) cc_final: 0.8616 (m-10) REVERT: A 149 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8697 (tt) REVERT: A 199 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 219 PHE cc_start: 0.7715 (t80) cc_final: 0.7107 (m-10) REVERT: A 252 LEU cc_start: 0.8881 (mt) cc_final: 0.8559 (mt) REVERT: A 305 LYS cc_start: 0.8973 (mmtt) cc_final: 0.8693 (mmmt) REVERT: A 360 ASP cc_start: 0.8819 (t70) cc_final: 0.8364 (t0) REVERT: A 362 TYR cc_start: 0.9048 (t80) cc_final: 0.8692 (t80) REVERT: A 381 PHE cc_start: 0.8376 (t80) cc_final: 0.7854 (t80) outliers start: 26 outliers final: 21 residues processed: 201 average time/residue: 0.1503 time to fit residues: 41.1111 Evaluate side-chains 215 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 383 ASP 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 61 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 HIS B 47 GLN B 398 HIS ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 6286 Z= 0.275 Angle : 0.625 8.352 8544 Z= 0.324 Chirality : 0.044 0.173 978 Planarity : 0.005 0.042 1040 Dihedral : 9.791 81.684 898 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 6.50 % Allowed : 25.53 % Favored : 67.98 % 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: 2.48 (0.30), residues: 756 helix: 2.06 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 0.40 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.004 0.001 HIS B 315 PHE 0.031 0.002 PHE A 234 TYR 0.015 0.001 TYR B 201 ARG 0.006 0.000 ARG A 50 *********************** 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 243 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.684 Fit side-chains REVERT: B 69 GLN cc_start: 0.8302 (tp40) cc_final: 0.8067 (tp40) REVERT: B 78 ARG cc_start: 0.8540 (mmm160) cc_final: 0.8105 (mmm-85) REVERT: B 149 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8748 (tt) REVERT: B 199 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8286 (tm-30) REVERT: B 252 LEU cc_start: 0.8938 (mt) cc_final: 0.8635 (mt) REVERT: B 360 ASP cc_start: 0.8849 (t70) cc_final: 0.8411 (t0) REVERT: B 362 TYR cc_start: 0.9059 (t80) cc_final: 0.8683 (t80) REVERT: B 381 PHE cc_start: 0.8434 (t80) cc_final: 0.7970 (t80) REVERT: A 69 GLN cc_start: 0.8316 (tp40) cc_final: 0.8095 (tp40) REVERT: A 74 TRP cc_start: 0.7975 (t60) cc_final: 0.7745 (t60) REVERT: A 95 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8485 (mt) REVERT: A 149 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8714 (tt) REVERT: A 199 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8443 (tm-30) REVERT: A 252 LEU cc_start: 0.8930 (mt) cc_final: 0.8626 (mt) REVERT: A 360 ASP cc_start: 0.8843 (t70) cc_final: 0.8407 (t0) REVERT: A 362 TYR cc_start: 0.9070 (t80) cc_final: 0.8705 (t80) REVERT: A 381 PHE cc_start: 0.8443 (t80) cc_final: 0.7975 (t80) outliers start: 43 outliers final: 32 residues processed: 222 average time/residue: 0.1804 time to fit residues: 52.3012 Evaluate side-chains 229 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 389 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 24 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.0980 chunk 38 optimal weight: 9.9990 chunk 70 optimal weight: 0.0070 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6286 Z= 0.170 Angle : 0.601 10.414 8544 Z= 0.305 Chirality : 0.041 0.155 978 Planarity : 0.005 0.040 1040 Dihedral : 9.505 79.525 898 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.47 % Allowed : 28.25 % Favored : 68.28 % 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: 2.79 (0.30), residues: 756 helix: 2.23 (0.21), residues: 572 sheet: None (None), residues: 0 loop : 0.74 (0.50), residues: 184 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 0.025 0.001 PHE B 234 TYR 0.013 0.001 TYR A 201 ARG 0.007 0.000 ARG B 50 *********************** 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 212 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.714 Fit side-chains REVERT: B 37 GLN cc_start: 0.7569 (mt0) cc_final: 0.7279 (mp10) REVERT: B 50 ARG cc_start: 0.8266 (ttm110) cc_final: 0.7533 (ttt180) REVERT: B 69 GLN cc_start: 0.8188 (tp40) cc_final: 0.7946 (tp40) REVERT: B 199 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8220 (tm-30) REVERT: B 252 LEU cc_start: 0.8950 (mt) cc_final: 0.8630 (mt) REVERT: B 305 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8762 (mmmt) REVERT: B 360 ASP cc_start: 0.8806 (t70) cc_final: 0.8336 (t0) REVERT: B 362 TYR cc_start: 0.9003 (t80) cc_final: 0.8619 (t80) REVERT: B 369 GLU cc_start: 0.7471 (mp0) cc_final: 0.7157 (mt-10) REVERT: B 381 PHE cc_start: 0.8390 (t80) cc_final: 0.7805 (t80) REVERT: A 37 GLN cc_start: 0.7648 (mt0) cc_final: 0.7330 (mp10) REVERT: A 69 GLN cc_start: 0.8262 (tp40) cc_final: 0.8028 (tp40) REVERT: A 74 TRP cc_start: 0.7963 (t60) cc_final: 0.7709 (t60) REVERT: A 199 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8425 (tm-30) REVERT: A 247 LYS cc_start: 0.7780 (tttt) cc_final: 0.7432 (tttt) REVERT: A 252 LEU cc_start: 0.8904 (mt) cc_final: 0.8602 (mt) REVERT: A 305 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8765 (mmmt) REVERT: A 362 TYR cc_start: 0.8984 (t80) cc_final: 0.8704 (t80) REVERT: A 381 PHE cc_start: 0.8394 (t80) cc_final: 0.7810 (t80) outliers start: 23 outliers final: 17 residues processed: 204 average time/residue: 0.1679 time to fit residues: 45.4388 Evaluate side-chains 196 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 383 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 GLN A 46 HIS A 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6286 Z= 0.200 Angle : 0.613 9.609 8544 Z= 0.312 Chirality : 0.042 0.181 978 Planarity : 0.005 0.041 1040 Dihedral : 9.281 79.675 894 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.38 % Allowed : 27.19 % Favored : 68.43 % 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: 2.69 (0.30), residues: 756 helix: 2.18 (0.21), residues: 572 sheet: None (None), residues: 0 loop : 0.60 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 74 HIS 0.004 0.001 HIS B 315 PHE 0.015 0.001 PHE B 187 TYR 0.020 0.001 TYR A 387 ARG 0.009 0.001 ARG A 50 *********************** 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 211 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.763 Fit side-chains REVERT: B 37 GLN cc_start: 0.7669 (mt0) cc_final: 0.7294 (mp10) REVERT: B 69 GLN cc_start: 0.8191 (tp40) cc_final: 0.7951 (tp40) REVERT: B 199 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8435 (tm-30) REVERT: B 252 LEU cc_start: 0.8972 (mt) cc_final: 0.8658 (mt) REVERT: B 305 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8678 (mmmt) REVERT: B 329 LYS cc_start: 0.7993 (tttp) cc_final: 0.7713 (tttm) REVERT: B 360 ASP cc_start: 0.8844 (t70) cc_final: 0.8371 (t0) REVERT: B 362 TYR cc_start: 0.8993 (t80) cc_final: 0.8656 (t80) REVERT: B 369 GLU cc_start: 0.7457 (mp0) cc_final: 0.7184 (mt-10) REVERT: B 381 PHE cc_start: 0.8392 (t80) cc_final: 0.7811 (t80) REVERT: A 37 GLN cc_start: 0.7685 (mt0) cc_final: 0.7328 (mp10) REVERT: A 50 ARG cc_start: 0.8341 (ttm110) cc_final: 0.7698 (ttt180) REVERT: A 69 GLN cc_start: 0.8314 (tp40) cc_final: 0.8072 (tp40) REVERT: A 74 TRP cc_start: 0.7936 (t60) cc_final: 0.7680 (t60) REVERT: A 199 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8433 (tm-30) REVERT: A 252 LEU cc_start: 0.8975 (mt) cc_final: 0.8657 (mt) REVERT: A 305 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8777 (mmmt) REVERT: A 362 TYR cc_start: 0.8995 (t80) cc_final: 0.8740 (t80) REVERT: A 381 PHE cc_start: 0.8424 (t80) cc_final: 0.7836 (t80) outliers start: 29 outliers final: 26 residues processed: 200 average time/residue: 0.1695 time to fit residues: 45.8233 Evaluate side-chains 204 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 GLN A 46 HIS A 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6286 Z= 0.214 Angle : 0.661 11.713 8544 Z= 0.325 Chirality : 0.042 0.178 978 Planarity : 0.005 0.043 1040 Dihedral : 9.199 79.101 894 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.38 % Allowed : 27.19 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.30), residues: 756 helix: 2.14 (0.21), residues: 572 sheet: None (None), residues: 0 loop : 0.47 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 74 HIS 0.004 0.001 HIS B 315 PHE 0.038 0.001 PHE A 234 TYR 0.020 0.001 TYR A 387 ARG 0.007 0.000 ARG B 50 *********************** 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 216 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.721 Fit side-chains REVERT: B 69 GLN cc_start: 0.8208 (tp40) cc_final: 0.7966 (tp40) REVERT: B 199 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8436 (tm-30) REVERT: B 252 LEU cc_start: 0.8971 (mt) cc_final: 0.8659 (mt) REVERT: B 329 LYS cc_start: 0.8011 (tttp) cc_final: 0.7797 (tttm) REVERT: B 360 ASP cc_start: 0.8818 (t70) cc_final: 0.8337 (t0) REVERT: B 362 TYR cc_start: 0.8976 (t80) cc_final: 0.8597 (t80) REVERT: B 369 GLU cc_start: 0.7463 (mp0) cc_final: 0.7224 (mt-10) REVERT: B 381 PHE cc_start: 0.8404 (t80) cc_final: 0.7821 (t80) REVERT: A 74 TRP cc_start: 0.7925 (t60) cc_final: 0.7667 (t60) REVERT: A 199 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8462 (tm-30) REVERT: A 252 LEU cc_start: 0.8985 (mt) cc_final: 0.8682 (mt) REVERT: A 305 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8790 (mmmt) REVERT: A 362 TYR cc_start: 0.8999 (t80) cc_final: 0.8672 (t80) REVERT: A 381 PHE cc_start: 0.8471 (t80) cc_final: 0.8042 (t80) outliers start: 29 outliers final: 27 residues processed: 204 average time/residue: 0.1559 time to fit residues: 42.9160 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 : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 365 SER 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: 0.5980 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 GLN A 46 HIS A 174 GLN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6286 Z= 0.194 Angle : 0.654 10.690 8544 Z= 0.322 Chirality : 0.042 0.172 978 Planarity : 0.005 0.042 1040 Dihedral : 9.118 79.124 894 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.53 % Allowed : 27.95 % Favored : 67.52 % 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 (0.30), residues: 756 helix: 2.16 (0.21), residues: 572 sheet: None (None), residues: 0 loop : 0.46 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 74 HIS 0.004 0.001 HIS A 46 PHE 0.016 0.001 PHE B 187 TYR 0.019 0.001 TYR A 387 ARG 0.008 0.001 ARG A 50 *********************** 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 211 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.775 Fit side-chains REVERT: B 199 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8414 (tm-30) REVERT: B 252 LEU cc_start: 0.8966 (mt) cc_final: 0.8656 (mt) REVERT: B 305 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8783 (mmmt) REVERT: B 329 LYS cc_start: 0.8010 (tttp) cc_final: 0.7786 (tttm) REVERT: B 345 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.7061 (m170) REVERT: B 360 ASP cc_start: 0.8820 (t70) cc_final: 0.8331 (t0) REVERT: B 362 TYR cc_start: 0.8923 (t80) cc_final: 0.8634 (t80) REVERT: B 369 GLU cc_start: 0.7380 (mp0) cc_final: 0.7173 (mt-10) REVERT: B 381 PHE cc_start: 0.8390 (t80) cc_final: 0.7811 (t80) REVERT: A 50 ARG cc_start: 0.8321 (ttm110) cc_final: 0.7691 (ttt180) REVERT: A 74 TRP cc_start: 0.7907 (t60) cc_final: 0.7658 (t60) REVERT: A 199 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8431 (tm-30) REVERT: A 252 LEU cc_start: 0.8982 (mt) cc_final: 0.8653 (mt) REVERT: A 305 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8798 (mmmt) REVERT: A 362 TYR cc_start: 0.8962 (t80) cc_final: 0.8716 (t80) REVERT: A 381 PHE cc_start: 0.8452 (t80) cc_final: 0.8022 (t80) outliers start: 30 outliers final: 28 residues processed: 199 average time/residue: 0.1486 time to fit residues: 40.7646 Evaluate side-chains 202 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 0.0770 chunk 55 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 174 GLN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6286 Z= 0.192 Angle : 0.661 11.329 8544 Z= 0.326 Chirality : 0.042 0.178 978 Planarity : 0.005 0.042 1040 Dihedral : 9.061 79.267 894 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.68 % Allowed : 27.79 % Favored : 67.52 % 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: 2.54 (0.30), residues: 756 helix: 2.10 (0.21), residues: 572 sheet: None (None), residues: 0 loop : 0.48 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 74 HIS 0.004 0.001 HIS A 46 PHE 0.038 0.001 PHE A 234 TYR 0.019 0.001 TYR B 387 ARG 0.008 0.001 ARG A 50 ********************** 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 207 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.702 Fit side-chains REVERT: B 199 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8420 (tm-30) REVERT: B 252 LEU cc_start: 0.8975 (mt) cc_final: 0.8658 (mt) REVERT: B 305 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8747 (mmmt) REVERT: B 345 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.7028 (m170) REVERT: B 362 TYR cc_start: 0.8929 (t80) cc_final: 0.8588 (t80) REVERT: A 50 ARG cc_start: 0.8367 (ttm110) cc_final: 0.7713 (ttt180) REVERT: A 74 TRP cc_start: 0.7898 (t60) cc_final: 0.7637 (t60) REVERT: A 199 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8438 (tm-30) REVERT: A 244 ILE cc_start: 0.8326 (tp) cc_final: 0.7920 (mm) REVERT: A 252 LEU cc_start: 0.8937 (mt) cc_final: 0.8613 (mt) REVERT: A 305 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8777 (mmmt) REVERT: A 345 HIS cc_start: 0.7333 (OUTLIER) cc_final: 0.6949 (m170) REVERT: A 362 TYR cc_start: 0.8962 (t80) cc_final: 0.8595 (t80) REVERT: A 381 PHE cc_start: 0.8448 (t80) cc_final: 0.8020 (t80) outliers start: 31 outliers final: 29 residues processed: 192 average time/residue: 0.1443 time to fit residues: 38.2533 Evaluate side-chains 203 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 53 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN ** A 199 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 = 0.4017 r_free = 0.4017 target = 0.174219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137230 restraints weight = 7549.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142888 restraints weight = 3725.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.146553 restraints weight = 2430.774| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6286 Z= 0.185 Angle : 0.638 11.212 8544 Z= 0.317 Chirality : 0.041 0.179 978 Planarity : 0.005 0.042 1040 Dihedral : 9.022 79.435 894 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.93 % Allowed : 28.25 % Favored : 67.82 % 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: 2.64 (0.30), residues: 756 helix: 2.19 (0.21), residues: 572 sheet: None (None), residues: 0 loop : 0.43 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 74 HIS 0.004 0.001 HIS A 315 PHE 0.042 0.001 PHE B 234 TYR 0.019 0.001 TYR B 387 ARG 0.008 0.001 ARG B 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1580.00 seconds wall clock time: 30 minutes 34.92 seconds (1834.92 seconds total)