Starting phenix.real_space_refine on Fri May 9 15:46:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh0_44528/05_2025/9bh0_44528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh0_44528/05_2025/9bh0_44528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bh0_44528/05_2025/9bh0_44528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh0_44528/05_2025/9bh0_44528.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh0_44528/05_2025/9bh0_44528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh0_44528/05_2025/9bh0_44528.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 20 5.16 5 C 1940 2.51 5 N 458 2.21 5 O 516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2934 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2925 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 16, 'TRANS': 373} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 2.80, per 1000 atoms: 0.95 Number of scatterers: 2934 At special positions: 0 Unit cell: (69.139, 60.809, 79.968, 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 20 16.00 O 516 8.00 N 458 7.00 C 1940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 364.1 milliseconds 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 712 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 28 through 59 removed outlier: 4.030A pdb=" N GLY A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 60 through 94 removed outlier: 3.609A pdb=" N ARG A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 135 through 154 removed outlier: 3.782A pdb=" N GLY A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 180 removed outlier: 3.720A pdb=" N LYS A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.502A pdb=" N LEU A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 223 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 235 through 254 removed outlier: 5.328A pdb=" N GLU A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ALA A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 Proline residue: A 261 - end of helix removed outlier: 3.502A pdb=" N GLU A 268 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.604A pdb=" N PHE A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Proline residue: A 282 - end of helix removed outlier: 3.867A pdb=" N THR A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.504A pdb=" N TYR A 307 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 330 Processing helix chain 'A' and resid 335 through 349 removed outlier: 4.163A pdb=" N THR A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N MET A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 344 " --> pdb=" O MET A 340 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 348 " --> pdb=" O VAL A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 360 removed outlier: 4.236A pdb=" N ALA A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 388 removed outlier: 3.758A pdb=" N LEU A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 368 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 378 " --> pdb=" O VAL A 374 " (cutoff:3.500A) 232 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 897 1.34 - 1.46: 633 1.46 - 1.58: 1418 1.58 - 1.70: 0 1.70 - 1.81: 37 Bond restraints: 2985 Sorted by residual: bond pdb=" N ASP A1000 " pdb=" CA ASP A1000 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.64e+00 bond pdb=" CB GLU A 26 " pdb=" CG GLU A 26 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.15e+00 bond pdb=" N VAL A 272 " pdb=" CA VAL A 272 " ideal model delta sigma weight residual 1.468 1.461 0.008 1.05e-02 9.07e+03 5.45e-01 bond pdb=" CA GLU A 26 " pdb=" CB GLU A 26 " ideal model delta sigma weight residual 1.529 1.542 -0.013 1.78e-02 3.16e+03 5.03e-01 ... (remaining 2980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 3863 1.11 - 2.23: 149 2.23 - 3.34: 25 3.34 - 4.46: 15 4.46 - 5.57: 3 Bond angle restraints: 4055 Sorted by residual: angle pdb=" CA GLU A 26 " pdb=" CB GLU A 26 " pdb=" CG GLU A 26 " ideal model delta sigma weight residual 114.10 119.67 -5.57 2.00e+00 2.50e-01 7.75e+00 angle pdb=" N GLY A 154 " pdb=" CA GLY A 154 " pdb=" C GLY A 154 " ideal model delta sigma weight residual 111.24 115.23 -3.99 1.49e+00 4.50e-01 7.18e+00 angle pdb=" N THR A 286 " pdb=" CA THR A 286 " pdb=" C THR A 286 " ideal model delta sigma weight residual 114.56 111.16 3.40 1.27e+00 6.20e-01 7.16e+00 angle pdb=" C LEU A 221 " pdb=" N ILE A 222 " pdb=" CA ILE A 222 " ideal model delta sigma weight residual 122.66 120.46 2.20 9.70e-01 1.06e+00 5.15e+00 angle pdb=" CB GLU A 26 " pdb=" CG GLU A 26 " pdb=" CD GLU A 26 " ideal model delta sigma weight residual 112.60 116.32 -3.72 1.70e+00 3.46e-01 4.78e+00 ... (remaining 4050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 1570 15.93 - 31.86: 155 31.86 - 47.80: 36 47.80 - 63.73: 16 63.73 - 79.66: 1 Dihedral angle restraints: 1778 sinusoidal: 668 harmonic: 1110 Sorted by residual: dihedral pdb=" CA ILE A 42 " pdb=" C ILE A 42 " pdb=" N VAL A 43 " pdb=" CA VAL A 43 " ideal model delta harmonic sigma weight residual -180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ILE A 104 " pdb=" C ILE A 104 " pdb=" N HIS A 105 " pdb=" CA HIS A 105 " ideal model delta harmonic sigma weight residual -180.00 -162.56 -17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB MET A 247 " pdb=" CG MET A 247 " pdb=" SD MET A 247 " pdb=" CE MET A 247 " ideal model delta sinusoidal sigma weight residual -60.00 -3.47 -56.53 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 1775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 316 0.028 - 0.055: 121 0.055 - 0.083: 61 0.083 - 0.110: 13 0.110 - 0.138: 5 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA ILE A 104 " pdb=" N ILE A 104 " pdb=" C ILE A 104 " pdb=" CB ILE A 104 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE A 234 " pdb=" N ILE A 234 " pdb=" C ILE A 234 " pdb=" CB ILE A 234 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA VAL A 333 " pdb=" N VAL A 333 " pdb=" C VAL A 333 " pdb=" CB VAL A 333 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 513 not shown) Planarity restraints: 492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 109 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 110 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 265 " -0.110 9.50e-02 1.11e+02 4.94e-02 1.71e+00 pdb=" NE ARG A 265 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 265 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 265 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 265 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 110 " 0.004 2.00e-02 2.50e+03 8.59e-03 7.38e-01 pdb=" C PRO A 110 " -0.015 2.00e-02 2.50e+03 pdb=" O PRO A 110 " 0.006 2.00e-02 2.50e+03 pdb=" N ASN A 111 " 0.005 2.00e-02 2.50e+03 ... (remaining 489 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 25 2.64 - 3.20: 3007 3.20 - 3.77: 4576 3.77 - 4.33: 6085 4.33 - 4.90: 10223 Nonbonded interactions: 23916 Sorted by model distance: nonbonded pdb=" N GLU A 269 " pdb=" OE1 GLU A 269 " model vdw 2.071 3.120 nonbonded pdb=" OG SER A 114 " pdb=" OE1 GLU A 117 " model vdw 2.296 3.040 nonbonded pdb=" O ALA A 326 " pdb=" OG1 THR A 330 " model vdw 2.300 3.040 nonbonded pdb=" O ASN A 111 " pdb=" OD1 ASN A 111 " model vdw 2.430 3.040 nonbonded pdb=" O ARG A 265 " pdb=" OE1 GLU A 269 " model vdw 2.480 3.040 ... (remaining 23911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.550 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2985 Z= 0.142 Angle : 0.573 5.569 4055 Z= 0.324 Chirality : 0.037 0.138 516 Planarity : 0.004 0.049 492 Dihedral : 14.286 79.660 1066 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.32 % Allowed : 16.46 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.44), residues: 388 helix: 2.38 (0.29), residues: 309 sheet: None (None), residues: 0 loop : 0.07 (0.79), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 192 HIS 0.001 0.001 HIS A 109 PHE 0.009 0.001 PHE A 239 TYR 0.013 0.001 TYR A 4 ARG 0.008 0.001 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.14759 ( 232) hydrogen bonds : angle 5.63422 ( 690) covalent geometry : bond 0.00285 ( 2985) covalent geometry : angle 0.57252 ( 4055) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.6155 (mmt) REVERT: A 6 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8387 (mtmt) REVERT: A 40 LYS cc_start: 0.8401 (mttt) cc_final: 0.7524 (pttt) REVERT: A 62 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8684 (tptm) REVERT: A 94 LYS cc_start: 0.8579 (mttm) cc_final: 0.8245 (mtmt) REVERT: A 169 GLU cc_start: 0.8216 (mm-30) cc_final: 0.8002 (mt-10) REVERT: A 171 MET cc_start: 0.8126 (mmm) cc_final: 0.7905 (mmt) REVERT: A 223 VAL cc_start: 0.8469 (t) cc_final: 0.8124 (m) REVERT: A 254 CYS cc_start: 0.9097 (m) cc_final: 0.8539 (m) REVERT: A 286 THR cc_start: 0.8798 (p) cc_final: 0.8566 (t) REVERT: A 340 MET cc_start: 0.8702 (mmp) cc_final: 0.8290 (tpp) REVERT: A 362 ASP cc_start: 0.8244 (t70) cc_final: 0.7867 (t0) REVERT: A 387 THR cc_start: 0.8529 (m) cc_final: 0.8234 (p) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.2000 time to fit residues: 21.6207 Evaluate side-chains 85 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 0.1980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.090360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.080833 restraints weight = 5464.844| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.86 r_work: 0.2969 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2985 Z= 0.177 Angle : 0.612 5.370 4055 Z= 0.316 Chirality : 0.042 0.136 516 Planarity : 0.004 0.032 492 Dihedral : 4.645 40.652 410 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.80 % Allowed : 16.46 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.42), residues: 388 helix: 2.12 (0.28), residues: 319 sheet: None (None), residues: 0 loop : -0.48 (0.80), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.004 0.001 HIS A 105 PHE 0.020 0.002 PHE A 27 TYR 0.012 0.002 TYR A 197 ARG 0.002 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.05035 ( 232) hydrogen bonds : angle 4.39592 ( 690) covalent geometry : bond 0.00420 ( 2985) covalent geometry : angle 0.61214 ( 4055) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8452 (mmmm) REVERT: A 169 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8364 (mt-10) REVERT: A 171 MET cc_start: 0.8453 (mmm) cc_final: 0.8173 (mmt) REVERT: A 221 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7621 (mm) REVERT: A 223 VAL cc_start: 0.8805 (t) cc_final: 0.8490 (m) REVERT: A 241 LYS cc_start: 0.7627 (mmtp) cc_final: 0.7426 (tttp) REVERT: A 254 CYS cc_start: 0.9088 (m) cc_final: 0.8816 (m) REVERT: A 286 THR cc_start: 0.9143 (p) cc_final: 0.8889 (t) REVERT: A 340 MET cc_start: 0.8991 (mmp) cc_final: 0.8765 (tpp) outliers start: 12 outliers final: 6 residues processed: 90 average time/residue: 0.1639 time to fit residues: 17.4472 Evaluate side-chains 81 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 312 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.091692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.081819 restraints weight = 5369.584| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.86 r_work: 0.2987 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2985 Z= 0.144 Angle : 0.555 5.288 4055 Z= 0.285 Chirality : 0.040 0.139 516 Planarity : 0.004 0.031 492 Dihedral : 4.106 22.189 407 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 4.11 % Allowed : 18.04 % Favored : 77.85 % 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 (0.43), residues: 388 helix: 2.15 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -0.47 (0.86), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.002 0.001 HIS A 105 PHE 0.023 0.002 PHE A 279 TYR 0.012 0.002 TYR A 75 ARG 0.001 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 232) hydrogen bonds : angle 4.21046 ( 690) covalent geometry : bond 0.00329 ( 2985) covalent geometry : angle 0.55484 ( 4055) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8415 (mmmm) REVERT: A 104 ILE cc_start: 0.7794 (mt) cc_final: 0.7287 (tt) REVERT: A 126 ASN cc_start: 0.8433 (t0) cc_final: 0.8230 (t0) REVERT: A 133 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7832 (mm-30) REVERT: A 171 MET cc_start: 0.8380 (mmm) cc_final: 0.8162 (mmt) REVERT: A 221 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7615 (mp) REVERT: A 223 VAL cc_start: 0.8799 (t) cc_final: 0.8510 (m) REVERT: A 254 CYS cc_start: 0.8993 (m) cc_final: 0.8737 (m) REVERT: A 286 THR cc_start: 0.9096 (p) cc_final: 0.8849 (t) REVERT: A 340 MET cc_start: 0.8976 (mmp) cc_final: 0.8751 (tpp) outliers start: 13 outliers final: 7 residues processed: 83 average time/residue: 0.1591 time to fit residues: 15.6304 Evaluate side-chains 80 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 317 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.0030 chunk 16 optimal weight: 0.9980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.090188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.080426 restraints weight = 5366.086| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.85 r_work: 0.2965 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2985 Z= 0.187 Angle : 0.565 5.363 4055 Z= 0.292 Chirality : 0.041 0.130 516 Planarity : 0.004 0.034 492 Dihedral : 4.126 23.405 407 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.75 % Allowed : 18.99 % Favored : 76.27 % 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: 2.36 (0.43), residues: 388 helix: 1.99 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.58 (0.86), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 192 HIS 0.003 0.001 HIS A 5 PHE 0.023 0.002 PHE A 27 TYR 0.012 0.002 TYR A 197 ARG 0.001 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 232) hydrogen bonds : angle 4.22590 ( 690) covalent geometry : bond 0.00449 ( 2985) covalent geometry : angle 0.56533 ( 4055) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8579 (mtmt) cc_final: 0.7969 (pttt) REVERT: A 104 ILE cc_start: 0.7771 (mt) cc_final: 0.7318 (tt) REVERT: A 126 ASN cc_start: 0.8466 (t0) cc_final: 0.8241 (t0) REVERT: A 133 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 223 VAL cc_start: 0.8832 (t) cc_final: 0.8558 (m) REVERT: A 286 THR cc_start: 0.9095 (p) cc_final: 0.8885 (t) REVERT: A 340 MET cc_start: 0.9045 (mmp) cc_final: 0.8801 (tpp) outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 0.1486 time to fit residues: 14.4575 Evaluate side-chains 78 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.090237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.080268 restraints weight = 5274.461| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.84 r_work: 0.2955 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2985 Z= 0.196 Angle : 0.569 5.414 4055 Z= 0.295 Chirality : 0.042 0.129 516 Planarity : 0.004 0.035 492 Dihedral : 4.169 24.151 407 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.43 % Allowed : 19.62 % Favored : 75.95 % 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: 2.29 (0.43), residues: 388 helix: 1.94 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.62 (0.87), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 192 HIS 0.003 0.001 HIS A 5 PHE 0.024 0.002 PHE A 279 TYR 0.011 0.001 TYR A 197 ARG 0.002 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.04714 ( 232) hydrogen bonds : angle 4.24174 ( 690) covalent geometry : bond 0.00474 ( 2985) covalent geometry : angle 0.56931 ( 4055) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7802 (mt) cc_final: 0.7358 (tt) REVERT: A 126 ASN cc_start: 0.8472 (t0) cc_final: 0.8220 (t0) REVERT: A 133 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 223 VAL cc_start: 0.8836 (t) cc_final: 0.8551 (m) REVERT: A 340 MET cc_start: 0.9074 (mmp) cc_final: 0.8819 (tpp) REVERT: A 383 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8595 (mp) outliers start: 14 outliers final: 7 residues processed: 82 average time/residue: 0.1953 time to fit residues: 19.1177 Evaluate side-chains 77 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.080676 restraints weight = 5377.152| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.88 r_work: 0.2964 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2985 Z= 0.176 Angle : 0.566 5.397 4055 Z= 0.292 Chirality : 0.041 0.128 516 Planarity : 0.004 0.038 492 Dihedral : 4.105 23.464 407 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 4.11 % Allowed : 21.52 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.43), residues: 388 helix: 1.98 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.73 (0.87), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 192 HIS 0.002 0.001 HIS A 5 PHE 0.026 0.002 PHE A 27 TYR 0.009 0.001 TYR A 197 ARG 0.003 0.000 ARG A 386 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 232) hydrogen bonds : angle 4.17553 ( 690) covalent geometry : bond 0.00420 ( 2985) covalent geometry : angle 0.56561 ( 4055) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7819 (mt) cc_final: 0.7378 (tt) REVERT: A 126 ASN cc_start: 0.8502 (t0) cc_final: 0.8296 (t0) REVERT: A 133 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7898 (mm-30) REVERT: A 223 VAL cc_start: 0.8854 (t) cc_final: 0.8584 (m) REVERT: A 340 MET cc_start: 0.9064 (mmp) cc_final: 0.8814 (tpp) REVERT: A 367 MET cc_start: 0.8261 (mtt) cc_final: 0.8004 (mtm) REVERT: A 383 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8607 (mp) outliers start: 13 outliers final: 8 residues processed: 80 average time/residue: 0.1496 time to fit residues: 14.3656 Evaluate side-chains 76 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 11 optimal weight: 0.0970 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 22 optimal weight: 0.0870 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 overall best weight: 0.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.092982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.082882 restraints weight = 5317.212| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.89 r_work: 0.3004 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2985 Z= 0.128 Angle : 0.563 5.963 4055 Z= 0.290 Chirality : 0.040 0.131 516 Planarity : 0.004 0.039 492 Dihedral : 3.944 22.666 407 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.16 % Allowed : 22.78 % Favored : 74.05 % 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: 2.68 (0.44), residues: 388 helix: 2.20 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.41 (0.91), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.002 0.001 HIS A 5 PHE 0.028 0.002 PHE A 27 TYR 0.017 0.001 TYR A 4 ARG 0.001 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 232) hydrogen bonds : angle 4.03036 ( 690) covalent geometry : bond 0.00291 ( 2985) covalent geometry : angle 0.56315 ( 4055) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7773 (mt) cc_final: 0.7336 (tt) REVERT: A 126 ASN cc_start: 0.8471 (t0) cc_final: 0.8264 (t0) REVERT: A 133 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7897 (mm-30) REVERT: A 223 VAL cc_start: 0.8815 (t) cc_final: 0.8528 (m) REVERT: A 340 MET cc_start: 0.9036 (mmp) cc_final: 0.8795 (tpp) REVERT: A 383 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8610 (mp) outliers start: 10 outliers final: 7 residues processed: 78 average time/residue: 0.1576 time to fit residues: 14.6766 Evaluate side-chains 78 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.0470 chunk 3 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.092645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.082626 restraints weight = 5270.277| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.84 r_work: 0.2999 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2985 Z= 0.152 Angle : 0.589 6.231 4055 Z= 0.303 Chirality : 0.040 0.125 516 Planarity : 0.004 0.034 492 Dihedral : 3.869 22.139 407 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.80 % Allowed : 23.10 % Favored : 73.10 % 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: 2.72 (0.44), residues: 388 helix: 2.21 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.27 (0.94), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 192 HIS 0.002 0.001 HIS A 5 PHE 0.031 0.002 PHE A 27 TYR 0.016 0.001 TYR A 4 ARG 0.001 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 232) hydrogen bonds : angle 4.03935 ( 690) covalent geometry : bond 0.00364 ( 2985) covalent geometry : angle 0.58864 ( 4055) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7797 (mt) cc_final: 0.7358 (tt) REVERT: A 133 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7912 (mm-30) REVERT: A 223 VAL cc_start: 0.8826 (t) cc_final: 0.8546 (m) REVERT: A 340 MET cc_start: 0.9068 (mmp) cc_final: 0.8813 (tpp) REVERT: A 383 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8615 (mp) outliers start: 12 outliers final: 9 residues processed: 76 average time/residue: 0.1551 time to fit residues: 14.1977 Evaluate side-chains 84 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 32 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.082779 restraints weight = 5276.045| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.84 r_work: 0.2998 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2985 Z= 0.150 Angle : 0.588 6.388 4055 Z= 0.304 Chirality : 0.041 0.126 516 Planarity : 0.004 0.034 492 Dihedral : 3.856 21.853 407 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.48 % Allowed : 24.68 % 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: 2.62 (0.44), residues: 388 helix: 2.17 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.51 (0.92), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 192 HIS 0.002 0.001 HIS A 105 PHE 0.030 0.002 PHE A 27 TYR 0.015 0.001 TYR A 4 ARG 0.001 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 232) hydrogen bonds : angle 4.08227 ( 690) covalent geometry : bond 0.00357 ( 2985) covalent geometry : angle 0.58779 ( 4055) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7770 (mt) cc_final: 0.7312 (tt) REVERT: A 126 ASN cc_start: 0.8432 (t0) cc_final: 0.8192 (t0) REVERT: A 133 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7905 (mm-30) REVERT: A 169 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8256 (tt0) REVERT: A 179 MET cc_start: 0.8645 (mmp) cc_final: 0.8370 (mmp) REVERT: A 223 VAL cc_start: 0.8819 (t) cc_final: 0.8539 (m) REVERT: A 340 MET cc_start: 0.9069 (mmp) cc_final: 0.8802 (tpp) REVERT: A 383 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8605 (mp) outliers start: 11 outliers final: 7 residues processed: 80 average time/residue: 0.1430 time to fit residues: 13.8495 Evaluate side-chains 75 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.091570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.081625 restraints weight = 5246.413| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.84 r_work: 0.2981 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 2985 Z= 0.182 Angle : 0.623 7.075 4055 Z= 0.323 Chirality : 0.042 0.124 516 Planarity : 0.004 0.035 492 Dihedral : 3.931 21.942 407 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.16 % Allowed : 24.68 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.44), residues: 388 helix: 2.06 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.44 (0.94), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 192 HIS 0.003 0.001 HIS A 5 PHE 0.030 0.002 PHE A 27 TYR 0.022 0.002 TYR A 4 ARG 0.001 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 232) hydrogen bonds : angle 4.12819 ( 690) covalent geometry : bond 0.00445 ( 2985) covalent geometry : angle 0.62319 ( 4055) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7768 (mt) cc_final: 0.7307 (tt) REVERT: A 133 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7905 (mm-30) REVERT: A 179 MET cc_start: 0.8651 (mmp) cc_final: 0.8381 (mmp) REVERT: A 199 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8160 (tp) REVERT: A 223 VAL cc_start: 0.8833 (t) cc_final: 0.8550 (m) REVERT: A 340 MET cc_start: 0.9076 (mmp) cc_final: 0.8793 (tpp) REVERT: A 383 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8385 (mp) REVERT: A 387 THR cc_start: 0.8663 (t) cc_final: 0.8399 (p) outliers start: 10 outliers final: 8 residues processed: 76 average time/residue: 0.1356 time to fit residues: 12.6163 Evaluate side-chains 77 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.0030 chunk 36 optimal weight: 0.1980 chunk 34 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.093176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.083272 restraints weight = 5170.834| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.82 r_work: 0.3018 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2985 Z= 0.144 Angle : 0.613 6.983 4055 Z= 0.315 Chirality : 0.041 0.127 516 Planarity : 0.004 0.034 492 Dihedral : 3.884 21.672 407 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 3.16 % Allowed : 25.32 % Favored : 71.52 % 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: 2.67 (0.44), residues: 388 helix: 2.20 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.50 (0.92), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.002 0.001 HIS A 105 PHE 0.029 0.002 PHE A 27 TYR 0.020 0.001 TYR A 4 ARG 0.001 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 232) hydrogen bonds : angle 4.05661 ( 690) covalent geometry : bond 0.00345 ( 2985) covalent geometry : angle 0.61292 ( 4055) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1920.20 seconds wall clock time: 33 minutes 57.51 seconds (2037.51 seconds total)