Starting phenix.real_space_refine on Sat Apr 26 18:10:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh0_44528/04_2025/9bh0_44528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh0_44528/04_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_44528/04_2025/9bh0_44528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh0_44528/04_2025/9bh0_44528.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh0_44528/04_2025/9bh0_44528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh0_44528/04_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-5669/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: 2.76, per 1000 atoms: 0.94 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: 0.77 Conformation dependent library (CDL) restraints added in 367.5 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: 0.29 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: 0.78 Time building geometry restraints manager: 0.91 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: 2.140 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: 12.380 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- 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 : 0.295 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: 0.1786 time to fit residues: 18.9595 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 : 0.308 ------------------------------------------------------------------------------- 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: 0.0980 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: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.090473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.080928 restraints weight = 5470.128| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.86 r_work: 0.2970 rms_B_bonded: 2.30 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: 0.8275 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2985 Z= 0.177 Angle : 0.605 5.348 4055 Z= 0.313 Chirality : 0.042 0.133 516 Planarity : 0.004 0.031 492 Dihedral : 4.597 40.111 410 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.80 % Allowed : 16.14 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.42), residues: 388 helix: 2.16 (0.28), residues: 319 sheet: None (None), residues: 0 loop : -0.42 (0.81), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.003 0.001 HIS A 105 PHE 0.020 0.002 PHE A 27 TYR 0.013 0.002 TYR A 197 ARG 0.002 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.05093 ( 232) hydrogen bonds : angle 4.41150 ( 690) covalent geometry : bond 0.00415 ( 2985) covalent geometry : angle 0.60472 ( 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 : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6882 (mmt) cc_final: 0.6559 (mmt) REVERT: A 62 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8476 (mmmm) REVERT: A 126 ASN cc_start: 0.8422 (t0) cc_final: 0.8139 (t0) REVERT: A 129 GLU cc_start: 0.8236 (tt0) cc_final: 0.7980 (tt0) REVERT: A 133 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 169 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8368 (mt-10) REVERT: A 171 MET cc_start: 0.8451 (mmm) cc_final: 0.8175 (mmt) REVERT: A 221 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7613 (mm) REVERT: A 223 VAL cc_start: 0.8799 (t) cc_final: 0.8497 (m) REVERT: A 241 LYS cc_start: 0.7716 (mmtp) cc_final: 0.7427 (tttp) REVERT: A 254 CYS cc_start: 0.9123 (m) cc_final: 0.8851 (m) REVERT: A 286 THR cc_start: 0.9150 (p) cc_final: 0.8899 (t) REVERT: A 340 MET cc_start: 0.8985 (mmp) cc_final: 0.8758 (tpp) outliers start: 12 outliers final: 6 residues processed: 90 average time/residue: 0.1737 time to fit residues: 18.5312 Evaluate side-chains 82 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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: 0.4980 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.091341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.081431 restraints weight = 5371.073| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.86 r_work: 0.2977 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2985 Z= 0.155 Angle : 0.550 5.321 4055 Z= 0.285 Chirality : 0.041 0.138 516 Planarity : 0.004 0.031 492 Dihedral : 4.112 22.271 407 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.94 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: 2.49 (0.43), residues: 388 helix: 2.08 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -0.41 (0.87), 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 0.022 0.002 PHE A 27 TYR 0.011 0.002 TYR A 75 ARG 0.001 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 232) hydrogen bonds : angle 4.23653 ( 690) covalent geometry : bond 0.00357 ( 2985) covalent geometry : angle 0.54967 ( 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 : 0.331 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8424 (mmmm) REVERT: A 104 ILE cc_start: 0.7795 (mt) cc_final: 0.7289 (tt) REVERT: A 126 ASN cc_start: 0.8447 (t0) cc_final: 0.8232 (t0) REVERT: A 133 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7842 (mm-30) REVERT: A 169 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8387 (mt-10) REVERT: A 171 MET cc_start: 0.8397 (mmm) cc_final: 0.8169 (mmt) REVERT: A 221 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7595 (mt) REVERT: A 223 VAL cc_start: 0.8801 (t) cc_final: 0.8507 (m) REVERT: A 254 CYS cc_start: 0.9002 (m) cc_final: 0.8745 (m) REVERT: A 286 THR cc_start: 0.9094 (p) cc_final: 0.8858 (t) REVERT: A 340 MET cc_start: 0.8985 (mmp) cc_final: 0.8753 (tpp) outliers start: 13 outliers final: 7 residues processed: 83 average time/residue: 0.1730 time to fit residues: 16.9950 Evaluate side-chains 81 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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: 0.8980 chunk 36 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.090715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080843 restraints weight = 5349.354| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.85 r_work: 0.2973 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2985 Z= 0.170 Angle : 0.555 5.366 4055 Z= 0.289 Chirality : 0.041 0.129 516 Planarity : 0.004 0.033 492 Dihedral : 4.078 23.470 407 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.43 % Allowed : 18.99 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.43), residues: 388 helix: 2.01 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.59 (0.86), 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 0.023 0.002 PHE A 27 TYR 0.014 0.002 TYR A 4 ARG 0.001 0.000 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 232) hydrogen bonds : angle 4.19756 ( 690) covalent geometry : bond 0.00404 ( 2985) covalent geometry : angle 0.55464 ( 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 91 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6958 (mmt) cc_final: 0.6725 (tpt) REVERT: A 40 LYS cc_start: 0.8577 (mtmt) cc_final: 0.7966 (pttt) REVERT: A 62 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8394 (mmmm) REVERT: A 104 ILE cc_start: 0.7769 (mt) cc_final: 0.7309 (tt) REVERT: A 126 ASN cc_start: 0.8459 (t0) cc_final: 0.8222 (t0) REVERT: A 133 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7863 (mm-30) REVERT: A 223 VAL cc_start: 0.8820 (t) cc_final: 0.8542 (m) REVERT: A 340 MET cc_start: 0.9028 (mmp) cc_final: 0.8790 (tpp) outliers start: 14 outliers final: 9 residues processed: 84 average time/residue: 0.1558 time to fit residues: 15.7981 Evaluate side-chains 79 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS 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 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: 0.4980 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 8 optimal weight: 0.0970 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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 = 0.091653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.081821 restraints weight = 5308.906| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.81 r_work: 0.2994 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2985 Z= 0.147 Angle : 0.540 5.369 4055 Z= 0.281 Chirality : 0.040 0.131 516 Planarity : 0.004 0.034 492 Dihedral : 4.048 23.953 407 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 4.43 % Allowed : 20.57 % 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: 2.46 (0.43), residues: 388 helix: 2.09 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.72 (0.86), 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 0.025 0.002 PHE A 279 TYR 0.017 0.001 TYR A 4 ARG 0.001 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 232) hydrogen bonds : angle 4.11749 ( 690) covalent geometry : bond 0.00345 ( 2985) covalent geometry : angle 0.54025 ( 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 89 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6907 (mmt) cc_final: 0.6690 (tpt) REVERT: A 104 ILE cc_start: 0.7808 (mt) cc_final: 0.7366 (tt) REVERT: A 126 ASN cc_start: 0.8471 (t0) cc_final: 0.8261 (t0) REVERT: A 133 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7857 (mm-30) REVERT: A 169 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8267 (tt0) REVERT: A 179 MET cc_start: 0.8768 (mmm) cc_final: 0.8507 (mmp) REVERT: A 223 VAL cc_start: 0.8808 (t) cc_final: 0.8533 (m) REVERT: A 340 MET cc_start: 0.9026 (mmp) cc_final: 0.8789 (tpp) REVERT: A 367 MET cc_start: 0.8168 (mtt) cc_final: 0.7964 (mtm) outliers start: 14 outliers final: 7 residues processed: 81 average time/residue: 0.1640 time to fit residues: 15.8954 Evaluate side-chains 77 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 254 CYS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 317 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 chunk 14 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.091357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.081182 restraints weight = 5376.777| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.88 r_work: 0.2974 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2726 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= 0.161 Angle : 0.553 5.378 4055 Z= 0.288 Chirality : 0.040 0.128 516 Planarity : 0.004 0.040 492 Dihedral : 3.970 23.012 407 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.80 % Allowed : 21.20 % 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: 2.55 (0.43), residues: 388 helix: 2.16 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -0.60 (0.89), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 192 HIS 0.002 0.001 HIS A 5 PHE 0.027 0.002 PHE A 27 TYR 0.013 0.001 TYR A 4 ARG 0.001 0.000 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 232) hydrogen bonds : angle 4.12145 ( 690) covalent geometry : bond 0.00385 ( 2985) covalent geometry : angle 0.55266 ( 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 88 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7040 (mmt) cc_final: 0.6835 (tpt) REVERT: A 91 ASN cc_start: 0.9065 (m-40) cc_final: 0.8847 (m-40) REVERT: A 104 ILE cc_start: 0.7812 (mt) cc_final: 0.7360 (tt) REVERT: A 133 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7924 (mm-30) REVERT: A 223 VAL cc_start: 0.8857 (t) cc_final: 0.8591 (m) REVERT: A 340 MET cc_start: 0.9058 (mmp) cc_final: 0.8812 (tpp) REVERT: A 367 MET cc_start: 0.8166 (mtt) cc_final: 0.7953 (mtm) REVERT: A 383 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8621 (mp) outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 0.1572 time to fit residues: 16.0574 Evaluate side-chains 83 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 254 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3252 r_free = 0.3252 target = 0.090684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.080663 restraints weight = 5357.914| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.85 r_work: 0.2961 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2985 Z= 0.197 Angle : 0.596 5.900 4055 Z= 0.312 Chirality : 0.041 0.126 516 Planarity : 0.004 0.035 492 Dihedral : 4.012 22.860 407 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.43 % Allowed : 21.52 % 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: 2.37 (0.43), residues: 388 helix: 2.04 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.78 (0.90), residues: 66 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 0.011 0.001 TYR A 4 ARG 0.001 0.000 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 232) hydrogen bonds : angle 4.19755 ( 690) covalent geometry : bond 0.00473 ( 2985) covalent geometry : angle 0.59620 ( 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 89 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7158 (mmt) cc_final: 0.6941 (tpt) REVERT: A 91 ASN cc_start: 0.9067 (m-40) cc_final: 0.8848 (m-40) REVERT: A 104 ILE cc_start: 0.7809 (mt) cc_final: 0.7372 (tt) REVERT: A 133 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7929 (mm-30) REVERT: A 169 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8293 (tt0) REVERT: A 179 MET cc_start: 0.8742 (mmm) cc_final: 0.8412 (mmp) REVERT: A 223 VAL cc_start: 0.8846 (t) cc_final: 0.8584 (m) REVERT: A 340 MET cc_start: 0.9071 (mmp) cc_final: 0.8816 (tpp) REVERT: A 367 MET cc_start: 0.8235 (mtt) cc_final: 0.8022 (mtm) REVERT: A 383 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8599 (mp) outliers start: 14 outliers final: 12 residues processed: 82 average time/residue: 0.1535 time to fit residues: 15.1842 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 : 0.475 ------------------------------------------------------------------------------- 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 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 317 LEU Chi-restraints excluded: chain A residue 333 VAL 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: 0.0980 chunk 24 optimal weight: 0.4980 chunk 14 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 16 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 overall best weight: 0.2578 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.092634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.082601 restraints weight = 5265.353| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.85 r_work: 0.3003 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2985 Z= 0.139 Angle : 0.586 6.648 4055 Z= 0.301 Chirality : 0.040 0.128 516 Planarity : 0.004 0.034 492 Dihedral : 3.892 22.327 407 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 3.80 % Allowed : 23.73 % Favored : 72.47 % 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: 2.90 (0.44), residues: 388 helix: 2.37 (0.28), residues: 316 sheet: None (None), residues: 0 loop : -0.13 (0.91), residues: 72 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 0.027 0.002 PHE A 27 TYR 0.013 0.001 TYR A 4 ARG 0.001 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 232) hydrogen bonds : angle 4.08458 ( 690) covalent geometry : bond 0.00325 ( 2985) covalent geometry : angle 0.58614 ( 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 85 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7763 (mt) cc_final: 0.7319 (tt) REVERT: A 133 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7923 (mm-30) REVERT: A 179 MET cc_start: 0.8735 (mmm) cc_final: 0.8420 (mmp) REVERT: A 223 VAL cc_start: 0.8826 (t) cc_final: 0.8554 (m) REVERT: A 340 MET cc_start: 0.9042 (mmp) cc_final: 0.8802 (tpp) REVERT: A 367 MET cc_start: 0.8125 (mtt) cc_final: 0.7895 (mtm) REVERT: A 383 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8621 (mp) outliers start: 12 outliers final: 9 residues processed: 79 average time/residue: 0.1511 time to fit residues: 14.3252 Evaluate side-chains 88 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 317 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: 0.9980 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.092081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.082080 restraints weight = 5298.806| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.84 r_work: 0.2993 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2958 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= 0.155 Angle : 0.593 6.855 4055 Z= 0.305 Chirality : 0.040 0.126 516 Planarity : 0.004 0.034 492 Dihedral : 3.906 22.071 407 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 3.80 % Allowed : 23.42 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.44), residues: 388 helix: 2.30 (0.28), residues: 316 sheet: None (None), residues: 0 loop : -0.13 (0.91), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 192 HIS 0.002 0.001 HIS A 105 PHE 0.030 0.002 PHE A 27 TYR 0.012 0.001 TYR A 4 ARG 0.003 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 232) hydrogen bonds : angle 4.08830 ( 690) covalent geometry : bond 0.00366 ( 2985) covalent geometry : angle 0.59307 ( 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 82 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7758 (mt) cc_final: 0.7306 (tt) REVERT: A 133 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7917 (mm-30) REVERT: A 223 VAL cc_start: 0.8833 (t) cc_final: 0.8564 (m) REVERT: A 340 MET cc_start: 0.9062 (mmp) cc_final: 0.8816 (tpp) REVERT: A 383 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8616 (mp) outliers start: 12 outliers final: 10 residues processed: 76 average time/residue: 0.1513 time to fit residues: 14.0098 Evaluate side-chains 80 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 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 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 317 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: 0.8980 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.0060 chunk 38 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.091416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.081502 restraints weight = 5265.097| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.82 r_work: 0.2982 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2985 Z= 0.180 Angle : 0.618 7.200 4055 Z= 0.317 Chirality : 0.041 0.124 516 Planarity : 0.004 0.034 492 Dihedral : 3.931 22.121 407 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.16 % Allowed : 24.05 % Favored : 72.78 % 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: 2.71 (0.44), residues: 388 helix: 2.23 (0.28), residues: 316 sheet: None (None), residues: 0 loop : -0.16 (0.91), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 192 HIS 0.002 0.001 HIS A 105 PHE 0.029 0.002 PHE A 27 TYR 0.010 0.001 TYR A 4 ARG 0.003 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 232) hydrogen bonds : angle 4.15118 ( 690) covalent geometry : bond 0.00433 ( 2985) covalent geometry : angle 0.61792 ( 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 82 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 104 ILE cc_start: 0.7765 (mt) cc_final: 0.7293 (tt) REVERT: A 133 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7949 (mm-30) REVERT: A 223 VAL cc_start: 0.8835 (t) cc_final: 0.8561 (m) REVERT: A 340 MET cc_start: 0.9069 (mmp) cc_final: 0.8802 (tpp) REVERT: A 383 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8610 (mp) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 0.1559 time to fit residues: 14.8548 Evaluate side-chains 86 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 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 317 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: 1.9990 chunk 36 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 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 = 0.3265 r_free = 0.3265 target = 0.091613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.081661 restraints weight = 5209.420| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.83 r_work: 0.2986 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 2985 Z= 0.182 Angle : 0.639 7.256 4055 Z= 0.327 Chirality : 0.042 0.124 516 Planarity : 0.004 0.034 492 Dihedral : 3.958 22.194 407 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.48 % Allowed : 24.37 % 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: 2.75 (0.44), residues: 388 helix: 2.26 (0.28), residues: 316 sheet: None (None), residues: 0 loop : -0.13 (0.91), residues: 72 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 0.029 0.002 PHE A 27 TYR 0.019 0.001 TYR A 4 ARG 0.003 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 232) hydrogen bonds : angle 4.16029 ( 690) covalent geometry : bond 0.00445 ( 2985) covalent geometry : angle 0.63907 ( 4055) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2061.96 seconds wall clock time: 36 minutes 0.44 seconds (2160.44 seconds total)