Starting phenix.real_space_refine on Tue Aug 4 14:26:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26va_80903/08_2026/26va_80903.cif Found real_map, /net/cci-nas-00/data/ceres_data/26va_80903/08_2026/26va_80903.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/26va_80903/08_2026/26va_80903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26va_80903/08_2026/26va_80903.map" model { file = "/net/cci-nas-00/data/ceres_data/26va_80903/08_2026/26va_80903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26va_80903/08_2026/26va_80903.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.041 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 33 5.16 5 C 2569 2.51 5 N 611 2.21 5 O 647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3860 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3844 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 22, 'TRANS': 477} Chain breaks: 1 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.09, per 1000 atoms: 0.28 Number of scatterers: 3860 At special positions: 0 Unit cell: (80.51, 68.06, 73.87, 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 33 16.00 O 647 8.00 N 611 7.00 C 2569 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: 0.32 Conformation dependent library (CDL) restraints added in 139.8 milliseconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 902 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 82.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 26 through 49 removed outlier: 3.824A pdb=" N VAL A 31 " --> pdb=" O MET A 27 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.364A pdb=" N PHE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 97 through 100 Processing helix chain 'A' and resid 101 through 110 removed outlier: 3.922A pdb=" N CYS A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 108 " --> pdb=" O CYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 3.668A pdb=" N VAL A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 138 through 173 removed outlier: 3.625A pdb=" N ARG A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 175 through 226 removed outlier: 3.748A pdb=" N TYR A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N LYS A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 238 removed outlier: 3.960A pdb=" N ARG A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 Processing helix chain 'A' and resid 274 through 282 removed outlier: 5.137A pdb=" N ARG A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 322 removed outlier: 4.104A pdb=" N PHE A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Proline residue: A 299 - end of helix Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.513A pdb=" N GLN A 330 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 removed outlier: 4.200A pdb=" N LEU A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 383 removed outlier: 3.701A pdb=" N ILE A 383 " --> pdb=" O MET A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 417 Processing helix chain 'A' and resid 422 through 434 Processing helix chain 'A' and resid 434 through 447 removed outlier: 3.638A pdb=" N LEU A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 476 removed outlier: 3.571A pdb=" N SER A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 549 removed outlier: 4.594A pdb=" N ALA A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 569 removed outlier: 3.585A pdb=" N LYS A 568 " --> pdb=" O PRO A 564 " (cutoff:3.500A) 285 hydrogen bonds defined for protein. 846 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: 0.44 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1081 1.34 - 1.46: 936 1.46 - 1.58: 1894 1.58 - 1.70: 1 1.70 - 1.82: 53 Bond restraints: 3965 Sorted by residual: bond pdb=" CB VAL A 538 " pdb=" CG1 VAL A 538 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.84e+00 bond pdb=" C4 BTN A 701 " pdb=" C5 BTN A 701 " ideal model delta sigma weight residual 1.558 1.599 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C PRO A 453 " pdb=" N PRO A 454 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.62e+00 bond pdb=" CB PRO A 89 " pdb=" CG PRO A 89 " ideal model delta sigma weight residual 1.492 1.417 0.075 5.00e-02 4.00e+02 2.27e+00 bond pdb=" C8 BTN A 701 " pdb=" C9 BTN A 701 " ideal model delta sigma weight residual 1.524 1.494 0.030 2.00e-02 2.50e+03 2.19e+00 ... (remaining 3960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 5051 1.64 - 3.29: 281 3.29 - 4.93: 49 4.93 - 6.58: 10 6.58 - 8.22: 10 Bond angle restraints: 5401 Sorted by residual: angle pdb=" N PRO A 453 " pdb=" CA PRO A 453 " pdb=" C PRO A 453 " ideal model delta sigma weight residual 110.70 114.87 -4.17 1.22e+00 6.72e-01 1.17e+01 angle pdb=" CA PRO A 453 " pdb=" C PRO A 453 " pdb=" N PRO A 454 " ideal model delta sigma weight residual 117.93 121.85 -3.92 1.20e+00 6.94e-01 1.07e+01 angle pdb=" CA TYR A 190 " pdb=" CB TYR A 190 " pdb=" CG TYR A 190 " ideal model delta sigma weight residual 113.90 119.45 -5.55 1.80e+00 3.09e-01 9.51e+00 angle pdb=" C LEU A 310 " pdb=" N ILE A 311 " pdb=" CA ILE A 311 " ideal model delta sigma weight residual 120.30 116.03 4.27 1.64e+00 3.72e-01 6.79e+00 angle pdb=" CA PRO A 164 " pdb=" N PRO A 164 " pdb=" CD PRO A 164 " ideal model delta sigma weight residual 112.00 108.38 3.62 1.40e+00 5.10e-01 6.68e+00 ... (remaining 5396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 2155 15.11 - 30.21: 90 30.21 - 45.32: 26 45.32 - 60.42: 3 60.42 - 75.53: 3 Dihedral angle restraints: 2277 sinusoidal: 853 harmonic: 1424 Sorted by residual: dihedral pdb=" CA ALA A 129 " pdb=" C ALA A 129 " pdb=" N TYR A 130 " pdb=" CA TYR A 130 " ideal model delta harmonic sigma weight residual -180.00 -156.67 -23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PRO A 388 " pdb=" C PRO A 388 " pdb=" N GLU A 389 " pdb=" CA GLU A 389 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR A 319 " pdb=" C TYR A 319 " pdb=" N GLN A 320 " pdb=" CA GLN A 320 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 380 0.041 - 0.081: 162 0.081 - 0.122: 67 0.122 - 0.162: 16 0.162 - 0.203: 5 Chirality restraints: 630 Sorted by residual: chirality pdb=" CB ILE A 311 " pdb=" CA ILE A 311 " pdb=" CG1 ILE A 311 " pdb=" CG2 ILE A 311 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU A 126 " pdb=" CB LEU A 126 " pdb=" CD1 LEU A 126 " pdb=" CD2 LEU A 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CA PHE A 298 " pdb=" N PHE A 298 " pdb=" C PHE A 298 " pdb=" CB PHE A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 627 not shown) Planarity restraints: 659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 371 " 0.020 2.00e-02 2.50e+03 2.11e-02 7.79e+00 pdb=" CG PHE A 371 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 371 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 371 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 371 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 371 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 371 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 442 " -0.006 2.00e-02 2.50e+03 1.61e-02 4.54e+00 pdb=" CG PHE A 442 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 442 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 442 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 442 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 442 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 442 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 259 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C LEU A 259 " 0.034 2.00e-02 2.50e+03 pdb=" O LEU A 259 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA A 260 " -0.011 2.00e-02 2.50e+03 ... (remaining 656 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1237 2.84 - 3.35: 3793 3.35 - 3.87: 6753 3.87 - 4.38: 7676 4.38 - 4.90: 13077 Nonbonded interactions: 32536 Sorted by model distance: nonbonded pdb=" O ASP A 203 " pdb=" OG1 THR A 207 " model vdw 2.320 3.040 nonbonded pdb=" OE1 GLU A 134 " pdb=" NH1 ARG A 142 " model vdw 2.329 3.120 nonbonded pdb=" OH TYR A 156 " pdb=" O11 BTN A 701 " model vdw 2.330 3.040 nonbonded pdb=" OH TYR A 132 " pdb=" O THR A 561 " model vdw 2.333 3.040 nonbonded pdb=" O ALA A 357 " pdb=" OG SER A 361 " model vdw 2.334 3.040 ... (remaining 32531 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.510 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.006 0.075 3965 Z= 0.271 Angle : 0.931 8.219 5401 Z= 0.499 Chirality : 0.053 0.203 630 Planarity : 0.008 0.045 659 Dihedral : 10.143 75.528 1375 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.28), residues: 496 helix: -2.24 (0.20), residues: 368 sheet: None (None), residues: 0 loop : -2.20 (0.47), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 142 TYR 0.028 0.003 TYR A 295 PHE 0.047 0.003 PHE A 371 TRP 0.020 0.002 TRP A 177 HIS 0.008 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.27 ( 3965) covalent geometry : angle 0.93135 / 0.50 ( 5401) hydrogen bonds : bond 0.10925 / 7.78 ( 285) hydrogen bonds : angle 6.62221 / 4.54 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.7987 (tttt) cc_final: 0.7037 (tptt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0710 time to fit residues: 5.5963 Evaluate side-chains 52 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN A 214 GLN A 238 HIS ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 372 ASN A 534 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.181322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152015 restraints weight = 4045.148| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.40 r_work: 0.3774 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3965 Z= 0.153 Angle : 0.604 8.843 5401 Z= 0.309 Chirality : 0.040 0.155 630 Planarity : 0.005 0.033 659 Dihedral : 5.846 51.393 560 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.96 % Allowed : 9.07 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.33), residues: 496 helix: -0.40 (0.24), residues: 373 sheet: None (None), residues: 0 loop : -2.43 (0.46), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 280 TYR 0.020 0.002 TYR A 106 PHE 0.019 0.002 PHE A 95 TRP 0.017 0.002 TRP A 177 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 3965) covalent geometry : angle 0.60447 / 0.31 ( 5401) hydrogen bonds : bond 0.04483 / 2.90 ( 285) hydrogen bonds : angle 4.91293 / 3.35 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.6965 (tt0) cc_final: 0.6735 (tt0) REVERT: A 66 MET cc_start: 0.6930 (mmm) cc_final: 0.6515 (mmt) REVERT: A 153 MET cc_start: 0.7212 (mmt) cc_final: 0.6978 (tpp) REVERT: A 238 HIS cc_start: 0.6097 (m-70) cc_final: 0.5885 (m90) REVERT: A 318 TYR cc_start: 0.8150 (t80) cc_final: 0.7901 (t80) REVERT: A 379 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.4752 (ttt) outliers start: 8 outliers final: 4 residues processed: 60 average time/residue: 0.0416 time to fit residues: 3.6433 Evaluate side-chains 52 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 465 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.0170 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.178675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.151064 restraints weight = 4018.892| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.22 r_work: 0.3606 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3965 Z= 0.143 Angle : 0.573 6.091 5401 Z= 0.290 Chirality : 0.039 0.154 630 Planarity : 0.004 0.033 659 Dihedral : 5.528 47.064 560 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.21 % Allowed : 9.80 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.36), residues: 496 helix: 0.32 (0.25), residues: 383 sheet: None (None), residues: 0 loop : -1.96 (0.50), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 280 TYR 0.020 0.002 TYR A 106 PHE 0.014 0.002 PHE A 95 TRP 0.013 0.001 TRP A 177 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 3965) covalent geometry : angle 0.57282 / 0.29 ( 5401) hydrogen bonds : bond 0.04282 / 2.76 ( 285) hydrogen bonds : angle 4.59191 / 3.14 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.6992 (mmm) cc_final: 0.6561 (mmt) REVERT: A 238 HIS cc_start: 0.6139 (m-70) cc_final: 0.5884 (m90) REVERT: A 379 MET cc_start: 0.6082 (mmp) cc_final: 0.4689 (ttt) outliers start: 9 outliers final: 8 residues processed: 58 average time/residue: 0.0276 time to fit residues: 2.2865 Evaluate side-chains 55 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 465 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.174519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.147019 restraints weight = 3989.029| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.30 r_work: 0.3588 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3965 Z= 0.156 Angle : 0.573 6.138 5401 Z= 0.292 Chirality : 0.040 0.141 630 Planarity : 0.004 0.032 659 Dihedral : 5.375 52.060 560 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.19 % Allowed : 10.29 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.36), residues: 496 helix: 0.67 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -1.73 (0.50), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 280 TYR 0.018 0.002 TYR A 106 PHE 0.013 0.002 PHE A 448 TRP 0.013 0.002 TRP A 177 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 3965) covalent geometry : angle 0.57298 / 0.29 ( 5401) hydrogen bonds : bond 0.04219 / 2.74 ( 285) hydrogen bonds : angle 4.50170 / 3.09 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.7142 (mmm) cc_final: 0.6781 (mmt) REVERT: A 238 HIS cc_start: 0.6216 (m-70) cc_final: 0.5994 (m90) REVERT: A 267 MET cc_start: 0.8252 (mmm) cc_final: 0.8043 (mmm) REVERT: A 379 MET cc_start: 0.6177 (mmp) cc_final: 0.4829 (ttt) outliers start: 13 outliers final: 8 residues processed: 59 average time/residue: 0.0378 time to fit residues: 3.1597 Evaluate side-chains 52 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 465 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 46 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.172664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143212 restraints weight = 4119.591| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.37 r_work: 0.3531 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3965 Z= 0.163 Angle : 0.575 6.244 5401 Z= 0.293 Chirality : 0.040 0.166 630 Planarity : 0.004 0.033 659 Dihedral : 5.375 58.005 560 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.92 % Allowed : 10.78 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.37), residues: 496 helix: 0.86 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.57 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 280 TYR 0.016 0.002 TYR A 190 PHE 0.010 0.002 PHE A 95 TRP 0.011 0.001 TRP A 100 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 3965) covalent geometry : angle 0.57538 / 0.29 ( 5401) hydrogen bonds : bond 0.04221 / 2.77 ( 285) hydrogen bonds : angle 4.50492 / 3.09 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.076 Fit side-chains REVERT: A 66 MET cc_start: 0.7231 (mmm) cc_final: 0.6870 (mmt) REVERT: A 238 HIS cc_start: 0.6236 (m-70) cc_final: 0.6009 (m90) REVERT: A 379 MET cc_start: 0.6221 (mmp) cc_final: 0.4854 (ttt) outliers start: 16 outliers final: 10 residues processed: 55 average time/residue: 0.0328 time to fit residues: 2.4936 Evaluate side-chains 56 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 561 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.173075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145214 restraints weight = 4067.548| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.33 r_work: 0.3524 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3965 Z= 0.148 Angle : 0.565 6.231 5401 Z= 0.288 Chirality : 0.039 0.154 630 Planarity : 0.004 0.036 659 Dihedral : 5.292 59.333 560 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.19 % Allowed : 11.76 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.37), residues: 496 helix: 1.03 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.35 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 64 TYR 0.018 0.002 TYR A 271 PHE 0.009 0.001 PHE A 95 TRP 0.011 0.001 TRP A 100 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 3965) covalent geometry : angle 0.56465 / 0.29 ( 5401) hydrogen bonds : bond 0.04079 / 2.66 ( 285) hydrogen bonds : angle 4.45456 / 3.05 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.6643 (mtt) cc_final: 0.6360 (mtt) REVERT: A 66 MET cc_start: 0.7144 (mmm) cc_final: 0.6765 (mmt) REVERT: A 238 HIS cc_start: 0.6208 (m-70) cc_final: 0.5984 (m90) REVERT: A 379 MET cc_start: 0.6182 (mmp) cc_final: 0.4805 (ttt) outliers start: 13 outliers final: 10 residues processed: 52 average time/residue: 0.0366 time to fit residues: 2.7911 Evaluate side-chains 52 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 561 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 0.0470 chunk 35 optimal weight: 0.0570 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.174234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.146825 restraints weight = 4078.519| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.31 r_work: 0.3616 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3965 Z= 0.140 Angle : 0.564 6.210 5401 Z= 0.284 Chirality : 0.039 0.175 630 Planarity : 0.004 0.033 659 Dihedral : 5.024 53.465 560 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.45 % Allowed : 12.99 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.37), residues: 496 helix: 1.18 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.27 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 64 TYR 0.023 0.002 TYR A 271 PHE 0.009 0.001 PHE A 95 TRP 0.010 0.001 TRP A 100 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 3965) covalent geometry : angle 0.56385 / 0.28 ( 5401) hydrogen bonds : bond 0.04001 / 2.61 ( 285) hydrogen bonds : angle 4.39421 / 3.01 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.6825 (mtt) cc_final: 0.6541 (mtt) REVERT: A 66 MET cc_start: 0.7343 (mmm) cc_final: 0.6943 (mmt) REVERT: A 238 HIS cc_start: 0.6467 (m-70) cc_final: 0.6230 (m90) outliers start: 10 outliers final: 9 residues processed: 49 average time/residue: 0.0420 time to fit residues: 3.0174 Evaluate side-chains 51 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 561 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.170171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.142522 restraints weight = 4067.955| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.28 r_work: 0.3534 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3965 Z= 0.170 Angle : 0.593 6.283 5401 Z= 0.300 Chirality : 0.040 0.174 630 Planarity : 0.004 0.032 659 Dihedral : 4.707 41.566 560 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.43 % Allowed : 12.50 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.37), residues: 496 helix: 1.15 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.22 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 280 TYR 0.020 0.002 TYR A 106 PHE 0.010 0.002 PHE A 265 TRP 0.013 0.001 TRP A 100 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 3965) covalent geometry : angle 0.59315 / 0.30 ( 5401) hydrogen bonds : bond 0.04164 / 2.72 ( 285) hydrogen bonds : angle 4.46760 / 3.06 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.6850 (mtt) cc_final: 0.6589 (mtt) REVERT: A 66 MET cc_start: 0.7236 (mmm) cc_final: 0.6782 (mmt) REVERT: A 238 HIS cc_start: 0.6382 (m-70) cc_final: 0.6119 (m90) outliers start: 14 outliers final: 11 residues processed: 54 average time/residue: 0.0433 time to fit residues: 3.4206 Evaluate side-chains 55 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 561 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.173178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.145909 restraints weight = 4032.126| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.29 r_work: 0.3638 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3965 Z= 0.149 Angle : 0.578 6.256 5401 Z= 0.291 Chirality : 0.039 0.166 630 Planarity : 0.004 0.033 659 Dihedral : 4.508 33.499 560 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.19 % Allowed : 12.75 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.37), residues: 496 helix: 1.21 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -1.18 (0.56), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 64 TYR 0.018 0.002 TYR A 106 PHE 0.008 0.001 PHE A 95 TRP 0.012 0.001 TRP A 100 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 3965) covalent geometry : angle 0.57823 / 0.29 ( 5401) hydrogen bonds : bond 0.04055 / 2.64 ( 285) hydrogen bonds : angle 4.43052 / 3.05 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.159 Fit side-chains REVERT: A 27 MET cc_start: 0.6861 (mtt) cc_final: 0.6613 (mtt) REVERT: A 66 MET cc_start: 0.7196 (mmm) cc_final: 0.6804 (mmt) REVERT: A 238 HIS cc_start: 0.6521 (m-70) cc_final: 0.6280 (m90) outliers start: 13 outliers final: 12 residues processed: 54 average time/residue: 0.0581 time to fit residues: 4.2758 Evaluate side-chains 55 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 561 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.0170 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.171450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.144437 restraints weight = 4062.030| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.26 r_work: 0.3514 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3965 Z= 0.167 Angle : 0.604 7.928 5401 Z= 0.303 Chirality : 0.040 0.164 630 Planarity : 0.004 0.033 659 Dihedral : 4.350 19.752 560 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.19 % Allowed : 12.75 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.38), residues: 496 helix: 1.21 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.21 (0.56), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 64 TYR 0.019 0.002 TYR A 106 PHE 0.008 0.001 PHE A 151 TRP 0.012 0.001 TRP A 100 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 3965) covalent geometry : angle 0.60353 / 0.30 ( 5401) hydrogen bonds : bond 0.04133 / 2.70 ( 285) hydrogen bonds : angle 4.46003 / 3.07 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.134 Fit side-chains REVERT: A 27 MET cc_start: 0.6915 (mtt) cc_final: 0.6660 (mtt) REVERT: A 66 MET cc_start: 0.7144 (mmm) cc_final: 0.6789 (mmt) REVERT: A 238 HIS cc_start: 0.6582 (m-70) cc_final: 0.6322 (m90) outliers start: 13 outliers final: 12 residues processed: 53 average time/residue: 0.0424 time to fit residues: 3.2821 Evaluate side-chains 57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 561 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.173536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146274 restraints weight = 4032.202| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.26 r_work: 0.3534 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3965 Z= 0.151 Angle : 0.602 9.336 5401 Z= 0.300 Chirality : 0.039 0.163 630 Planarity : 0.004 0.033 659 Dihedral : 4.315 18.615 560 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.43 % Allowed : 12.99 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.37), residues: 496 helix: 1.26 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -1.21 (0.55), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 64 TYR 0.024 0.002 TYR A 106 PHE 0.017 0.001 PHE A 95 TRP 0.012 0.001 TRP A 100 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 3965) covalent geometry : angle 0.60172 / 0.30 ( 5401) hydrogen bonds : bond 0.04084 / 2.67 ( 285) hydrogen bonds : angle 4.40270 / 3.04 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 941.46 seconds wall clock time: 16 minutes 56.29 seconds (1016.29 seconds total)