Starting phenix.real_space_refine on Tue Mar 11 14:32:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vq4_32085/03_2025/7vq4_32085.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vq4_32085/03_2025/7vq4_32085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vq4_32085/03_2025/7vq4_32085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vq4_32085/03_2025/7vq4_32085.map" model { file = "/net/cci-nas-00/data/ceres_data/7vq4_32085/03_2025/7vq4_32085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vq4_32085/03_2025/7vq4_32085.cif" } resolution = 3.2 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4070 2.51 5 N 1052 2.21 5 O 1150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6306 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Time building chain proxies: 4.13, per 1000 atoms: 0.65 Number of scatterers: 6306 At special positions: 0 Unit cell: (82.134, 84.162, 111.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1150 8.00 N 1052 7.00 C 4070 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: 1.66 Conformation dependent library (CDL) restraints added in 913.2 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 84.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 removed outlier: 3.624A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.863A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 Processing helix chain 'A' and resid 69 through 102 removed outlier: 3.756A pdb=" N THR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 125 Processing helix chain 'A' and resid 127 through 134 removed outlier: 3.524A pdb=" N LYS A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.601A pdb=" N SER A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 183 Processing helix chain 'A' and resid 187 through 214 removed outlier: 3.694A pdb=" N ASP A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 removed outlier: 4.615A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 267 through 293 removed outlier: 3.720A pdb=" N TYR A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 306 removed outlier: 3.833A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 removed outlier: 3.738A pdb=" N LEU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 removed outlier: 4.368A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 398 Processing helix chain 'B' and resid 2 through 18 removed outlier: 3.624A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.864A pdb=" N GLY B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 69 through 102 removed outlier: 3.757A pdb=" N THR B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 125 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.523A pdb=" N LYS B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.601A pdb=" N SER B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 183 Processing helix chain 'B' and resid 187 through 214 removed outlier: 3.693A pdb=" N ASP B 191 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.615A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 Processing helix chain 'B' and resid 267 through 293 removed outlier: 3.720A pdb=" N TYR B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 306 removed outlier: 3.833A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 330 removed outlier: 3.737A pdb=" N LEU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 330 " --> pdb=" O ILE B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 removed outlier: 4.368A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 398 509 hydrogen bonds defined for protein. 1527 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: 1.63 Time building geometry restraints manager: 1.95 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: 2008 1.34 - 1.46: 1045 1.46 - 1.57: 3321 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6434 Sorted by residual: bond pdb=" CB TRP B 57 " pdb=" CG TRP B 57 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.05e+00 bond pdb=" CB TRP A 57 " pdb=" CG TRP A 57 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 bond pdb=" CB TRP B 187 " pdb=" CG TRP B 187 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.63e+00 bond pdb=" CB TRP A 187 " pdb=" CG TRP A 187 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.62e+00 bond pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 1.527 1.518 0.009 8.50e-03 1.38e+04 1.14e+00 ... (remaining 6429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 8313 1.50 - 3.01: 299 3.01 - 4.51: 56 4.51 - 6.01: 20 6.01 - 7.52: 4 Bond angle restraints: 8692 Sorted by residual: angle pdb=" N VAL B 105 " pdb=" CA VAL B 105 " pdb=" C VAL B 105 " ideal model delta sigma weight residual 112.17 108.66 3.51 9.50e-01 1.11e+00 1.36e+01 angle pdb=" N VAL A 105 " pdb=" CA VAL A 105 " pdb=" C VAL A 105 " ideal model delta sigma weight residual 112.17 108.67 3.50 9.50e-01 1.11e+00 1.36e+01 angle pdb=" N PHE B 134 " pdb=" CA PHE B 134 " pdb=" C PHE B 134 " ideal model delta sigma weight residual 110.44 114.21 -3.77 1.20e+00 6.94e-01 9.89e+00 angle pdb=" N PHE A 134 " pdb=" CA PHE A 134 " pdb=" C PHE A 134 " ideal model delta sigma weight residual 110.44 114.16 -3.72 1.20e+00 6.94e-01 9.62e+00 angle pdb=" CA PRO B 267 " pdb=" C PRO B 267 " pdb=" O PRO B 267 " ideal model delta sigma weight residual 123.07 119.36 3.71 1.38e+00 5.25e-01 7.22e+00 ... (remaining 8687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 3396 18.03 - 36.05: 366 36.05 - 54.08: 62 54.08 - 72.10: 26 72.10 - 90.13: 6 Dihedral angle restraints: 3856 sinusoidal: 1532 harmonic: 2324 Sorted by residual: dihedral pdb=" CA CYS A 184 " pdb=" C CYS A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA CYS B 184 " pdb=" C CYS B 184 " pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta harmonic sigma weight residual -180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA HIS B 259 " pdb=" C HIS B 259 " pdb=" N GLY B 260 " pdb=" CA GLY B 260 " ideal model delta harmonic sigma weight residual -180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 499 0.030 - 0.060: 357 0.060 - 0.090: 105 0.090 - 0.119: 30 0.119 - 0.149: 5 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA PRO B 365 " pdb=" N PRO B 365 " pdb=" C PRO B 365 " pdb=" CB PRO B 365 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA PRO A 365 " pdb=" N PRO A 365 " pdb=" C PRO A 365 " pdb=" CB PRO A 365 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 332 " pdb=" N ILE A 332 " pdb=" C ILE A 332 " pdb=" CB ILE A 332 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 993 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 364 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 365 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 364 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO B 365 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 365 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 365 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 127 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 128 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 128 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 128 " 0.021 5.00e-02 4.00e+02 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 239 2.70 - 3.25: 6944 3.25 - 3.80: 10031 3.80 - 4.35: 11847 4.35 - 4.90: 20167 Nonbonded interactions: 49228 Sorted by model distance: nonbonded pdb=" OD1 ASP A 295 " pdb=" N PHE A 296 " model vdw 2.155 3.120 nonbonded pdb=" OD1 ASP B 295 " pdb=" N PHE B 296 " model vdw 2.155 3.120 nonbonded pdb=" O MET B 1 " pdb=" N ARG B 5 " model vdw 2.178 3.120 nonbonded pdb=" OH TYR A 291 " pdb=" OG SER B 376 " model vdw 2.209 3.040 nonbonded pdb=" NH1 ARG A 80 " pdb=" OH TYR A 136 " model vdw 2.225 3.120 ... (remaining 49223 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.150 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 0.044 6434 Z= 0.439 Angle : 0.740 7.518 8692 Z= 0.423 Chirality : 0.042 0.149 996 Planarity : 0.004 0.050 1090 Dihedral : 16.105 90.127 2352 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.30 % Allowed : 8.62 % Favored : 89.08 % 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: -1.96 (0.27), residues: 792 helix: -0.72 (0.18), residues: 666 sheet: None (None), residues: 0 loop : -3.76 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS B 266 PHE 0.018 0.002 PHE B 153 TYR 0.013 0.002 TYR B 291 ARG 0.003 0.001 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.724 Fit side-chains REVERT: A 40 TYR cc_start: 0.8043 (t80) cc_final: 0.7503 (t80) REVERT: A 180 SER cc_start: 0.9003 (t) cc_final: 0.8580 (p) REVERT: A 237 LYS cc_start: 0.8450 (mttt) cc_final: 0.8150 (mtmt) REVERT: A 306 LEU cc_start: 0.8688 (tp) cc_final: 0.8481 (tp) REVERT: A 307 GLU cc_start: 0.7515 (pt0) cc_final: 0.7258 (pm20) REVERT: A 322 LYS cc_start: 0.7820 (tptm) cc_final: 0.7412 (ttpt) REVERT: B 1 MET cc_start: 0.5033 (OUTLIER) cc_final: 0.4477 (ptp) REVERT: B 40 TYR cc_start: 0.8064 (t80) cc_final: 0.7540 (t80) REVERT: B 328 LEU cc_start: 0.9183 (tp) cc_final: 0.8902 (tp) outliers start: 16 outliers final: 7 residues processed: 216 average time/residue: 0.2278 time to fit residues: 60.9873 Evaluate side-chains 162 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 223 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS A 54 ASN A 251 ASN A 259 HIS A 293 ASN A 297 GLN A 340 HIS A 343 ASN B 24 HIS B 54 ASN B 251 ASN B 259 HIS B 280 GLN B 293 ASN B 297 GLN B 330 GLN B 340 HIS B 343 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.158101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129565 restraints weight = 9295.116| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.61 r_work: 0.3589 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6434 Z= 0.199 Angle : 0.562 5.791 8692 Z= 0.296 Chirality : 0.038 0.142 996 Planarity : 0.004 0.047 1090 Dihedral : 5.546 49.915 870 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.89 % Allowed : 15.66 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.30), residues: 792 helix: 1.55 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -3.20 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 57 HIS 0.003 0.001 HIS A 259 PHE 0.013 0.001 PHE A 145 TYR 0.014 0.001 TYR A 291 ARG 0.006 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8413 (pp30) REVERT: A 105 VAL cc_start: 0.6457 (OUTLIER) cc_final: 0.6079 (t) REVERT: A 159 MET cc_start: 0.7025 (ptt) cc_final: 0.6584 (mtm) REVERT: A 180 SER cc_start: 0.8991 (t) cc_final: 0.8406 (p) REVERT: A 193 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7185 (t-90) REVERT: A 237 LYS cc_start: 0.8380 (mttt) cc_final: 0.8020 (mtmt) REVERT: A 263 ARG cc_start: 0.8108 (tpp80) cc_final: 0.7209 (tmt170) REVERT: A 286 ASP cc_start: 0.8615 (t70) cc_final: 0.8342 (t0) REVERT: A 321 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7604 (mmt) REVERT: A 322 LYS cc_start: 0.7670 (tptm) cc_final: 0.7045 (ttpt) REVERT: A 368 MET cc_start: 0.8136 (mmm) cc_final: 0.7894 (mmm) REVERT: B 1 MET cc_start: 0.4655 (ttt) cc_final: 0.4259 (tpp) REVERT: B 9 ARG cc_start: 0.6221 (mtt-85) cc_final: 0.5436 (ptp90) REVERT: B 154 ARG cc_start: 0.7481 (mtp-110) cc_final: 0.7234 (mtm110) REVERT: B 193 HIS cc_start: 0.7719 (OUTLIER) cc_final: 0.7296 (t-90) REVERT: B 201 ASP cc_start: 0.8314 (t0) cc_final: 0.8006 (t0) REVERT: B 237 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7953 (mtmt) REVERT: B 328 LEU cc_start: 0.9060 (tp) cc_final: 0.8643 (tp) REVERT: B 377 MET cc_start: 0.8627 (mmt) cc_final: 0.8290 (mmm) outliers start: 34 outliers final: 19 residues processed: 186 average time/residue: 0.1763 time to fit residues: 43.0163 Evaluate side-chains 172 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.158866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.130185 restraints weight = 9750.299| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.51 r_work: 0.3644 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6434 Z= 0.188 Angle : 0.539 5.994 8692 Z= 0.280 Chirality : 0.037 0.160 996 Planarity : 0.004 0.048 1090 Dihedral : 4.546 36.441 866 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.75 % Allowed : 16.95 % Favored : 77.30 % 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: 2.15 (0.30), residues: 792 helix: 2.17 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -2.69 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 95 PHE 0.012 0.001 PHE B 141 TYR 0.011 0.001 TYR B 236 ARG 0.004 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8413 (pp30) REVERT: A 105 VAL cc_start: 0.6528 (OUTLIER) cc_final: 0.6211 (t) REVERT: A 159 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6606 (mtm) REVERT: A 180 SER cc_start: 0.9063 (t) cc_final: 0.8502 (p) REVERT: A 193 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.6955 (t-90) REVERT: A 201 ASP cc_start: 0.8297 (t0) cc_final: 0.8023 (t0) REVERT: A 237 LYS cc_start: 0.8451 (mttt) cc_final: 0.8093 (mtmt) REVERT: A 322 LYS cc_start: 0.7592 (tptm) cc_final: 0.6896 (ttpt) REVERT: B 1 MET cc_start: 0.5148 (ttt) cc_final: 0.4603 (tpp) REVERT: B 154 ARG cc_start: 0.7536 (mtp-110) cc_final: 0.7300 (mtm110) REVERT: B 193 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7230 (t-90) REVERT: B 237 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8143 (mtmt) REVERT: B 286 ASP cc_start: 0.8641 (t70) cc_final: 0.8426 (t0) REVERT: B 328 LEU cc_start: 0.9022 (tp) cc_final: 0.8606 (tp) outliers start: 40 outliers final: 24 residues processed: 182 average time/residue: 0.1653 time to fit residues: 40.2184 Evaluate side-chains 174 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 13 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.0270 chunk 15 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS A 330 GLN B 266 HIS B 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.159614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.130917 restraints weight = 9859.759| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.56 r_work: 0.3658 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6434 Z= 0.181 Angle : 0.543 7.090 8692 Z= 0.280 Chirality : 0.037 0.221 996 Planarity : 0.004 0.048 1090 Dihedral : 4.224 24.719 866 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.75 % Allowed : 18.53 % Favored : 75.72 % 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 (0.31), residues: 792 helix: 2.47 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.27 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.012 0.001 PHE B 141 TYR 0.014 0.001 TYR A 236 ARG 0.006 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8396 (pp30) REVERT: A 159 MET cc_start: 0.7117 (ptt) cc_final: 0.6650 (mtm) REVERT: A 193 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.6911 (t-90) REVERT: A 201 ASP cc_start: 0.8294 (t0) cc_final: 0.8024 (t0) REVERT: A 237 LYS cc_start: 0.8465 (mttt) cc_final: 0.8123 (mtmt) REVERT: A 321 MET cc_start: 0.7895 (mmt) cc_final: 0.7662 (mmt) REVERT: A 322 LYS cc_start: 0.7576 (tptm) cc_final: 0.6841 (ttpt) REVERT: A 331 MET cc_start: 0.8116 (tpp) cc_final: 0.7823 (tpp) REVERT: A 377 MET cc_start: 0.8462 (mmt) cc_final: 0.8216 (mmm) REVERT: B 1 MET cc_start: 0.5311 (ttt) cc_final: 0.4794 (tpp) REVERT: B 106 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6528 (tt0) REVERT: B 154 ARG cc_start: 0.7584 (mtp-110) cc_final: 0.7326 (mtm110) REVERT: B 193 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.7102 (t-90) REVERT: B 237 LYS cc_start: 0.8374 (mtmt) cc_final: 0.8151 (mtmt) REVERT: B 265 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7734 (mtp-110) REVERT: B 286 ASP cc_start: 0.8635 (t70) cc_final: 0.8429 (t0) REVERT: B 323 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7980 (mm-30) REVERT: B 328 LEU cc_start: 0.8939 (tp) cc_final: 0.8542 (tp) REVERT: B 377 MET cc_start: 0.8518 (mmt) cc_final: 0.8140 (mmm) outliers start: 40 outliers final: 25 residues processed: 176 average time/residue: 0.1740 time to fit residues: 40.2663 Evaluate side-chains 171 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 58 optimal weight: 0.0980 chunk 56 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 266 HIS B 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.158563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.130722 restraints weight = 9503.364| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.54 r_work: 0.3611 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6434 Z= 0.172 Angle : 0.540 7.173 8692 Z= 0.277 Chirality : 0.037 0.212 996 Planarity : 0.004 0.047 1090 Dihedral : 3.993 21.404 864 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.32 % Allowed : 19.68 % Favored : 75.00 % 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: 2.94 (0.31), residues: 792 helix: 2.65 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.00 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.011 0.001 PHE B 141 TYR 0.011 0.001 TYR A 236 ARG 0.005 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8397 (pp30) REVERT: A 159 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6677 (mtm) REVERT: A 193 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.6845 (t-90) REVERT: A 201 ASP cc_start: 0.8341 (t0) cc_final: 0.8054 (t0) REVERT: A 321 MET cc_start: 0.7761 (mmt) cc_final: 0.7477 (mmt) REVERT: A 322 LYS cc_start: 0.7499 (tptm) cc_final: 0.6774 (ttpt) REVERT: A 405 MET cc_start: 0.3217 (mpp) cc_final: 0.2651 (mmp) REVERT: B 1 MET cc_start: 0.5568 (ttt) cc_final: 0.5065 (tpp) REVERT: B 2 GLU cc_start: 0.6087 (mp0) cc_final: 0.5449 (mm-30) REVERT: B 154 ARG cc_start: 0.7541 (mtp-110) cc_final: 0.7215 (mtm110) REVERT: B 193 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7028 (t-90) REVERT: B 284 ARG cc_start: 0.8036 (mpt90) cc_final: 0.7820 (mpt90) REVERT: B 307 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7394 (pm20) REVERT: B 328 LEU cc_start: 0.8914 (tp) cc_final: 0.8469 (tp) REVERT: B 331 MET cc_start: 0.8102 (mmm) cc_final: 0.7863 (mmm) REVERT: B 405 MET cc_start: 0.2649 (mpp) cc_final: 0.2172 (mmp) outliers start: 37 outliers final: 28 residues processed: 180 average time/residue: 0.1706 time to fit residues: 40.6842 Evaluate side-chains 178 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 289 ASN B 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.152694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124475 restraints weight = 9595.498| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.52 r_work: 0.3535 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6434 Z= 0.280 Angle : 0.625 8.300 8692 Z= 0.320 Chirality : 0.039 0.206 996 Planarity : 0.004 0.052 1090 Dihedral : 4.152 21.097 862 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.89 % Allowed : 19.40 % Favored : 74.71 % 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: 2.56 (0.30), residues: 792 helix: 2.33 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -2.01 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.004 0.001 HIS B 95 PHE 0.012 0.002 PHE B 141 TYR 0.013 0.002 TYR A 236 ARG 0.007 0.001 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7312 (t-90) REVERT: A 96 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8467 (pp30) REVERT: A 159 MET cc_start: 0.7089 (ptt) cc_final: 0.6611 (mtm) REVERT: A 193 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7330 (t-90) REVERT: A 201 ASP cc_start: 0.8405 (t0) cc_final: 0.8140 (t0) REVERT: A 321 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7529 (mmt) REVERT: A 322 LYS cc_start: 0.7601 (tptm) cc_final: 0.6888 (ttpt) REVERT: A 368 MET cc_start: 0.7892 (mmm) cc_final: 0.7682 (mmm) REVERT: A 377 MET cc_start: 0.8682 (mmm) cc_final: 0.8475 (mmm) REVERT: B 1 MET cc_start: 0.5963 (ttt) cc_final: 0.5354 (tpp) REVERT: B 154 ARG cc_start: 0.7589 (mtp-110) cc_final: 0.7298 (mtm110) REVERT: B 193 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.7388 (t-90) REVERT: B 237 LYS cc_start: 0.8407 (mtmt) cc_final: 0.8151 (mtmt) REVERT: B 307 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7426 (pm20) REVERT: B 328 LEU cc_start: 0.8954 (tp) cc_final: 0.8589 (tp) REVERT: B 368 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7216 (tmm) REVERT: B 377 MET cc_start: 0.8630 (mmt) cc_final: 0.8265 (mmm) outliers start: 41 outliers final: 30 residues processed: 174 average time/residue: 0.1642 time to fit residues: 38.3077 Evaluate side-chains 174 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 0.0070 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** B 345 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 = 0.3990 r_free = 0.3990 target = 0.154907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.127094 restraints weight = 9414.708| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.50 r_work: 0.3573 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6434 Z= 0.204 Angle : 0.607 12.518 8692 Z= 0.300 Chirality : 0.038 0.203 996 Planarity : 0.004 0.050 1090 Dihedral : 4.111 23.414 862 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.03 % Allowed : 20.40 % Favored : 73.56 % 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: 2.82 (0.31), residues: 792 helix: 2.50 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.93 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 129 HIS 0.004 0.001 HIS B 259 PHE 0.011 0.001 PHE B 141 TYR 0.013 0.001 TYR B 236 ARG 0.007 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7203 (t-90) REVERT: A 96 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8477 (pp30) REVERT: A 159 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6599 (mtm) REVERT: A 193 HIS cc_start: 0.7760 (OUTLIER) cc_final: 0.7107 (t-90) REVERT: A 201 ASP cc_start: 0.8394 (t0) cc_final: 0.8149 (t0) REVERT: A 321 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7489 (mmt) REVERT: A 322 LYS cc_start: 0.7578 (tptm) cc_final: 0.6843 (ttpt) REVERT: A 331 MET cc_start: 0.8437 (mmm) cc_final: 0.8205 (mmm) REVERT: A 377 MET cc_start: 0.8749 (mmm) cc_final: 0.8541 (mmm) REVERT: A 405 MET cc_start: 0.3197 (mpp) cc_final: 0.2699 (mmp) REVERT: B 1 MET cc_start: 0.6080 (ttt) cc_final: 0.5641 (tpp) REVERT: B 154 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.7216 (mtm110) REVERT: B 193 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7224 (t-90) REVERT: B 237 LYS cc_start: 0.8349 (mtmt) cc_final: 0.8100 (mtmt) REVERT: B 368 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7172 (tmm) REVERT: B 377 MET cc_start: 0.8616 (mmt) cc_final: 0.8243 (mmm) outliers start: 42 outliers final: 29 residues processed: 166 average time/residue: 0.1660 time to fit residues: 36.9878 Evaluate side-chains 173 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 401 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 59 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 208 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.158126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.130435 restraints weight = 9411.903| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.51 r_work: 0.3616 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6434 Z= 0.174 Angle : 0.597 14.397 8692 Z= 0.291 Chirality : 0.037 0.201 996 Planarity : 0.003 0.047 1090 Dihedral : 3.998 25.000 862 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.60 % Allowed : 21.26 % Favored : 73.13 % 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: 3.04 (0.31), residues: 792 helix: 2.64 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.82 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.003 0.001 HIS A 259 PHE 0.011 0.001 PHE B 141 TYR 0.013 0.001 TYR B 236 ARG 0.006 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8420 (pp30) REVERT: A 159 MET cc_start: 0.7069 (ptt) cc_final: 0.6573 (mtm) REVERT: A 193 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.6875 (t-90) REVERT: A 201 ASP cc_start: 0.8362 (t0) cc_final: 0.8090 (t0) REVERT: A 321 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7449 (mmt) REVERT: A 322 LYS cc_start: 0.7528 (tptm) cc_final: 0.6764 (ttpt) REVERT: A 331 MET cc_start: 0.8441 (mmm) cc_final: 0.8081 (tpp) REVERT: A 377 MET cc_start: 0.8651 (mmm) cc_final: 0.8435 (mmm) REVERT: A 405 MET cc_start: 0.2822 (mpp) cc_final: 0.2312 (mmp) REVERT: B 1 MET cc_start: 0.5775 (ttt) cc_final: 0.5350 (tpp) REVERT: B 154 ARG cc_start: 0.7475 (mtp-110) cc_final: 0.7143 (mtm110) REVERT: B 193 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7111 (t-90) REVERT: B 237 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7990 (mtmt) REVERT: B 368 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7053 (tmm) REVERT: B 372 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8191 (mmt) outliers start: 39 outliers final: 30 residues processed: 172 average time/residue: 0.1590 time to fit residues: 36.9457 Evaluate side-chains 173 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 345 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 = 0.3962 r_free = 0.3962 target = 0.152431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.124563 restraints weight = 9634.642| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.51 r_work: 0.3539 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6434 Z= 0.269 Angle : 0.662 14.163 8692 Z= 0.328 Chirality : 0.039 0.202 996 Planarity : 0.004 0.050 1090 Dihedral : 4.159 22.507 862 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.46 % Allowed : 22.99 % Favored : 71.55 % 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: 2.72 (0.31), residues: 792 helix: 2.42 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.87 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 187 HIS 0.004 0.001 HIS B 95 PHE 0.012 0.001 PHE B 141 TYR 0.013 0.001 TYR B 236 ARG 0.006 0.001 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8277 (tp) cc_final: 0.8016 (mt) REVERT: A 95 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7237 (t-90) REVERT: A 96 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8459 (pp30) REVERT: A 159 MET cc_start: 0.7142 (ptt) cc_final: 0.6682 (mtm) REVERT: A 193 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7425 (t-90) REVERT: A 201 ASP cc_start: 0.8422 (t0) cc_final: 0.8172 (t0) REVERT: A 214 TYR cc_start: 0.7862 (t80) cc_final: 0.7637 (t80) REVERT: A 321 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7545 (mmt) REVERT: A 322 LYS cc_start: 0.7605 (tptm) cc_final: 0.6873 (ttpt) REVERT: A 331 MET cc_start: 0.8529 (mmm) cc_final: 0.8307 (mmm) REVERT: A 377 MET cc_start: 0.8765 (mmm) cc_final: 0.8460 (mmm) REVERT: A 405 MET cc_start: 0.3198 (mpp) cc_final: 0.2647 (mmp) REVERT: B 1 MET cc_start: 0.6417 (ttt) cc_final: 0.5762 (tpp) REVERT: B 154 ARG cc_start: 0.7516 (mtp-110) cc_final: 0.7191 (mtm110) REVERT: B 193 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7414 (t-90) REVERT: B 237 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8114 (mtmt) REVERT: B 368 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7269 (tmm) REVERT: B 377 MET cc_start: 0.8674 (mmt) cc_final: 0.8345 (mmm) outliers start: 38 outliers final: 31 residues processed: 174 average time/residue: 0.1600 time to fit residues: 37.7430 Evaluate side-chains 178 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 345 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 = 0.3990 r_free = 0.3990 target = 0.155364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127592 restraints weight = 9564.950| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.54 r_work: 0.3576 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6434 Z= 0.214 Angle : 0.643 14.462 8692 Z= 0.315 Chirality : 0.038 0.208 996 Planarity : 0.004 0.049 1090 Dihedral : 4.112 24.876 862 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.75 % Allowed : 22.41 % Favored : 71.84 % 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: 2.89 (0.31), residues: 792 helix: 2.53 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -1.81 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.004 0.001 HIS B 259 PHE 0.010 0.001 PHE B 141 TYR 0.013 0.001 TYR B 236 ARG 0.006 0.000 ARG B 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8288 (tp) cc_final: 0.8054 (mt) REVERT: A 95 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7208 (t-90) REVERT: A 96 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8455 (pp30) REVERT: A 159 MET cc_start: 0.7093 (ptt) cc_final: 0.6631 (mtm) REVERT: A 193 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7273 (t-90) REVERT: A 201 ASP cc_start: 0.8420 (t0) cc_final: 0.8172 (t0) REVERT: A 321 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7504 (mmt) REVERT: A 322 LYS cc_start: 0.7600 (tptm) cc_final: 0.6844 (ttpt) REVERT: A 331 MET cc_start: 0.8505 (mmm) cc_final: 0.8305 (mmm) REVERT: A 377 MET cc_start: 0.8701 (mmm) cc_final: 0.8469 (mmm) REVERT: A 405 MET cc_start: 0.2660 (mpp) cc_final: 0.2086 (mmp) REVERT: B 154 ARG cc_start: 0.7502 (mtp-110) cc_final: 0.7189 (mtm110) REVERT: B 193 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.7295 (t-90) REVERT: B 237 LYS cc_start: 0.8367 (mtmt) cc_final: 0.8068 (mtmt) REVERT: B 368 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.7196 (tmm) REVERT: B 377 MET cc_start: 0.8645 (mmt) cc_final: 0.8301 (mmm) outliers start: 40 outliers final: 29 residues processed: 169 average time/residue: 0.1583 time to fit residues: 36.0159 Evaluate side-chains 173 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 345 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 = 0.3980 r_free = 0.3980 target = 0.154405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126574 restraints weight = 9669.154| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.54 r_work: 0.3563 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6434 Z= 0.230 Angle : 0.651 14.203 8692 Z= 0.320 Chirality : 0.038 0.202 996 Planarity : 0.004 0.048 1090 Dihedral : 4.142 24.716 862 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.17 % Allowed : 22.84 % Favored : 71.98 % 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: 2.91 (0.30), residues: 792 helix: 2.56 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -1.77 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS A 259 PHE 0.011 0.001 PHE B 141 TYR 0.013 0.001 TYR B 236 ARG 0.006 0.000 ARG B 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2851.56 seconds wall clock time: 49 minutes 47.53 seconds (2987.53 seconds total)