Starting phenix.real_space_refine on Wed Sep 17 03:24:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7s_39826/09_2025/8z7s_39826.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7s_39826/09_2025/8z7s_39826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z7s_39826/09_2025/8z7s_39826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7s_39826/09_2025/8z7s_39826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z7s_39826/09_2025/8z7s_39826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7s_39826/09_2025/8z7s_39826.map" } resolution = 3.05 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= -0.002 sd= 0.116 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 16 5.16 5 C 2103 2.51 5 N 467 2.21 5 O 530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3116 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3098 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'VIB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.12, per 1000 atoms: 0.36 Number of scatterers: 3116 At special positions: 0 Unit cell: (62, 67, 68, 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 16 16.00 O 530 8.00 N 467 7.00 C 2103 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: 0.30 Conformation dependent library (CDL) restraints added in 133.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 86.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.507A pdb=" N ILE A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.760A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 79 through 99 removed outlier: 3.571A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 129 removed outlier: 3.947A pdb=" N THR A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 165 removed outlier: 3.656A pdb=" N ARG A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.513A pdb=" N PHE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 277 through 307 removed outlier: 4.222A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 337 removed outlier: 3.903A pdb=" N GLY A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 366 removed outlier: 3.502A pdb=" N THR A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 398 Processing helix chain 'A' and resid 402 through 426 removed outlier: 3.665A pdb=" N VAL A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 461 removed outlier: 3.737A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 741 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: 0.54 Time building geometry restraints manager: 0.40 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: 892 1.34 - 1.46: 733 1.46 - 1.57: 1557 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 3210 Sorted by residual: bond pdb=" N TYR A 445 " pdb=" CA TYR A 445 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.17e+00 bond pdb=" C2 VIB A 501 " pdb=" S1 VIB A 501 " ideal model delta sigma weight residual 1.670 1.715 -0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" N SER A 382 " pdb=" CA SER A 382 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.02e+00 bond pdb=" CA SER A 382 " pdb=" CB SER A 382 " ideal model delta sigma weight residual 1.529 1.506 0.023 1.55e-02 4.16e+03 2.15e+00 bond pdb=" CA LEU A 68 " pdb=" C LEU A 68 " ideal model delta sigma weight residual 1.520 1.536 -0.016 1.23e-02 6.61e+03 1.60e+00 ... (remaining 3205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 4254 1.28 - 2.55: 102 2.55 - 3.83: 19 3.83 - 5.10: 8 5.10 - 6.38: 5 Bond angle restraints: 4388 Sorted by residual: angle pdb=" N TYR A 445 " pdb=" CA TYR A 445 " pdb=" C TYR A 445 " ideal model delta sigma weight residual 111.07 108.25 2.82 1.07e+00 8.73e-01 6.97e+00 angle pdb=" CA SER A 382 " pdb=" C SER A 382 " pdb=" O SER A 382 " ideal model delta sigma weight residual 120.82 118.16 2.66 1.05e+00 9.07e-01 6.42e+00 angle pdb=" CA ASN A 399 " pdb=" CB ASN A 399 " pdb=" CG ASN A 399 " ideal model delta sigma weight residual 112.60 115.07 -2.47 1.00e+00 1.00e+00 6.08e+00 angle pdb=" CA TYR A 280 " pdb=" CB TYR A 280 " pdb=" CG TYR A 280 " ideal model delta sigma weight residual 113.90 118.11 -4.21 1.80e+00 3.09e-01 5.48e+00 angle pdb=" O SER A 382 " pdb=" C SER A 382 " pdb=" N TYR A 383 " ideal model delta sigma weight residual 122.07 124.46 -2.39 1.03e+00 9.43e-01 5.40e+00 ... (remaining 4383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 1533 16.59 - 33.19: 210 33.19 - 49.78: 50 49.78 - 66.37: 13 66.37 - 82.97: 6 Dihedral angle restraints: 1812 sinusoidal: 663 harmonic: 1149 Sorted by residual: dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ILE A 424 " pdb=" C ILE A 424 " pdb=" N VAL A 425 " pdb=" CA VAL A 425 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASP A 75 " pdb=" CB ASP A 75 " pdb=" CG ASP A 75 " pdb=" OD1 ASP A 75 " ideal model delta sinusoidal sigma weight residual -30.00 -85.07 55.07 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 1809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 330 0.034 - 0.067: 127 0.067 - 0.101: 31 0.101 - 0.134: 13 0.134 - 0.168: 4 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA ASN A 399 " pdb=" N ASN A 399 " pdb=" C ASN A 399 " pdb=" CB ASN A 399 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CB ILE A 127 " pdb=" CA ILE A 127 " pdb=" CG1 ILE A 127 " pdb=" CG2 ILE A 127 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA VAL A 261 " pdb=" N VAL A 261 " pdb=" C VAL A 261 " pdb=" CB VAL A 261 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 502 not shown) Planarity restraints: 525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 VIB A 501 " -0.148 2.00e-02 2.50e+03 2.61e-01 1.36e+03 pdb=" C4 VIB A 501 " -0.112 2.00e-02 2.50e+03 pdb=" C5 VIB A 501 " 0.039 2.00e-02 2.50e+03 pdb=" C6 VIB A 501 " 0.392 2.00e-02 2.50e+03 pdb=" C7A VIB A 501 " 0.393 2.00e-02 2.50e+03 pdb=" CM4 VIB A 501 " -0.384 2.00e-02 2.50e+03 pdb=" N3 VIB A 501 " 0.043 2.00e-02 2.50e+03 pdb=" S1 VIB A 501 " -0.222 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 150 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C ALA A 150 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA A 150 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 151 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 146 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C VAL A 146 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 146 " -0.010 2.00e-02 2.50e+03 pdb=" N THR A 147 " -0.009 2.00e-02 2.50e+03 ... (remaining 522 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 667 2.77 - 3.30: 3261 3.30 - 3.83: 5719 3.83 - 4.37: 6630 4.37 - 4.90: 11294 Nonbonded interactions: 27571 Sorted by model distance: nonbonded pdb=" OH TYR A 128 " pdb=" OG SER A 140 " model vdw 2.234 3.040 nonbonded pdb=" O VAL A 70 " pdb=" OG1 THR A 74 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR A 126 " pdb=" O PRO A 191 " model vdw 2.265 3.040 nonbonded pdb=" O GLN A 393 " pdb=" ND2 ASN A 397 " model vdw 2.319 3.120 nonbonded pdb=" NE2 GLN A 300 " pdb=" OE1 GLU A 320 " model vdw 2.320 3.120 ... (remaining 27566 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: 1.480 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.610 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.004 0.045 3210 Z= 0.191 Angle : 0.555 6.378 4388 Z= 0.308 Chirality : 0.041 0.168 505 Planarity : 0.012 0.261 525 Dihedral : 16.814 82.968 1078 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.30 % Allowed : 23.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.41), residues: 383 helix: 0.35 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.36 (0.94), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.018 0.001 TYR A 280 PHE 0.021 0.001 PHE A 71 TRP 0.010 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 3210) covalent geometry : angle 0.55524 ( 4388) hydrogen bonds : bond 0.16993 ( 247) hydrogen bonds : angle 7.19338 ( 741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.113 Fit side-chains REVERT: A 384 MET cc_start: 0.8982 (mmt) cc_final: 0.8611 (mmt) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.0590 time to fit residues: 3.4023 Evaluate side-chains 39 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3653 r_free = 0.3653 target = 0.143664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119812 restraints weight = 3379.171| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.51 r_work: 0.3246 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3210 Z= 0.165 Angle : 0.599 9.274 4388 Z= 0.316 Chirality : 0.042 0.164 505 Planarity : 0.004 0.031 525 Dihedral : 6.008 87.351 428 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.30 % Allowed : 19.82 % Favored : 76.88 % 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 aren not related in a simple way. whole: 2.11 (0.43), residues: 383 helix: 1.53 (0.28), residues: 325 sheet: None (None), residues: 0 loop : 1.08 (0.95), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.018 0.002 TYR A 280 PHE 0.020 0.002 PHE A 71 TRP 0.015 0.002 TRP A 94 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 3210) covalent geometry : angle 0.59923 ( 4388) hydrogen bonds : bond 0.05313 ( 247) hydrogen bonds : angle 4.53275 ( 741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.111 Fit side-chains REVERT: A 266 PHE cc_start: 0.7128 (m-80) cc_final: 0.6027 (t80) REVERT: A 437 ILE cc_start: 0.8543 (tp) cc_final: 0.8216 (tp) REVERT: A 458 MET cc_start: 0.7738 (mmp) cc_final: 0.7512 (mmm) outliers start: 11 outliers final: 5 residues processed: 54 average time/residue: 0.0505 time to fit residues: 3.6149 Evaluate side-chains 43 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 460 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3518 r_free = 0.3518 target = 0.133638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109449 restraints weight = 3488.266| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.56 r_work: 0.3190 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3210 Z= 0.172 Angle : 0.567 5.266 4388 Z= 0.304 Chirality : 0.043 0.173 505 Planarity : 0.004 0.033 525 Dihedral : 5.926 85.968 427 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.60 % Allowed : 20.72 % Favored : 75.68 % 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 aren not related in a simple way. whole: 2.16 (0.43), residues: 383 helix: 1.55 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 1.16 (0.95), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 78 TYR 0.017 0.002 TYR A 280 PHE 0.022 0.002 PHE A 71 TRP 0.015 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3210) covalent geometry : angle 0.56681 ( 4388) hydrogen bonds : bond 0.05060 ( 247) hydrogen bonds : angle 4.30835 ( 741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.119 Fit side-chains REVERT: A 458 MET cc_start: 0.7595 (mmp) cc_final: 0.7370 (mmm) outliers start: 12 outliers final: 10 residues processed: 51 average time/residue: 0.0468 time to fit residues: 3.1517 Evaluate side-chains 47 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 460 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN ** A 364 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 = 0.3625 r_free = 0.3625 target = 0.141300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117323 restraints weight = 3377.031| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.52 r_work: 0.3194 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3210 Z= 0.164 Angle : 0.549 5.249 4388 Z= 0.296 Chirality : 0.042 0.179 505 Planarity : 0.004 0.034 525 Dihedral : 5.846 83.750 427 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.60 % Allowed : 21.62 % Favored : 74.77 % 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 aren not related in a simple way. whole: 2.21 (0.43), residues: 383 helix: 1.55 (0.28), residues: 325 sheet: None (None), residues: 0 loop : 1.41 (0.97), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 402 TYR 0.019 0.002 TYR A 280 PHE 0.021 0.001 PHE A 71 TRP 0.015 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3210) covalent geometry : angle 0.54942 ( 4388) hydrogen bonds : bond 0.04886 ( 247) hydrogen bonds : angle 4.21595 ( 741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.112 Fit side-chains REVERT: A 164 LEU cc_start: 0.8628 (mt) cc_final: 0.8422 (mp) REVERT: A 384 MET cc_start: 0.8948 (mmt) cc_final: 0.8509 (mmt) REVERT: A 458 MET cc_start: 0.7629 (mmp) cc_final: 0.7417 (mmm) outliers start: 12 outliers final: 6 residues processed: 53 average time/residue: 0.0521 time to fit residues: 3.5962 Evaluate side-chains 45 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 444 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3620 r_free = 0.3620 target = 0.140777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116449 restraints weight = 3355.791| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.57 r_work: 0.3186 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3210 Z= 0.168 Angle : 0.550 5.270 4388 Z= 0.297 Chirality : 0.042 0.183 505 Planarity : 0.004 0.034 525 Dihedral : 5.817 83.063 427 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.40 % Allowed : 22.82 % Favored : 74.77 % 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 aren not related in a simple way. whole: 2.27 (0.43), residues: 383 helix: 1.58 (0.28), residues: 325 sheet: None (None), residues: 0 loop : 1.49 (0.98), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 402 TYR 0.018 0.002 TYR A 280 PHE 0.021 0.001 PHE A 71 TRP 0.016 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3210) covalent geometry : angle 0.54955 ( 4388) hydrogen bonds : bond 0.04902 ( 247) hydrogen bonds : angle 4.21580 ( 741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.133 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 0.0466 time to fit residues: 3.0943 Evaluate side-chains 47 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 444 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 chunk 17 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3637 r_free = 0.3637 target = 0.142154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117840 restraints weight = 3398.297| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.58 r_work: 0.3234 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3210 Z= 0.149 Angle : 0.549 7.975 4388 Z= 0.289 Chirality : 0.041 0.171 505 Planarity : 0.004 0.032 525 Dihedral : 5.756 82.406 427 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.60 % Allowed : 21.92 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.43), residues: 383 helix: 1.71 (0.28), residues: 325 sheet: None (None), residues: 0 loop : 1.56 (0.98), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 402 TYR 0.016 0.001 TYR A 280 PHE 0.020 0.001 PHE A 71 TRP 0.016 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3210) covalent geometry : angle 0.54913 ( 4388) hydrogen bonds : bond 0.04723 ( 247) hydrogen bonds : angle 4.12326 ( 741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.112 Fit side-chains REVERT: A 296 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 383 TYR cc_start: 0.8871 (t80) cc_final: 0.8606 (t80) REVERT: A 384 MET cc_start: 0.8969 (mmt) cc_final: 0.8596 (mmt) outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 0.0479 time to fit residues: 3.5059 Evaluate side-chains 52 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 457 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.0370 chunk 29 optimal weight: 0.0670 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3619 r_free = 0.3619 target = 0.142176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117694 restraints weight = 3379.006| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.63 r_work: 0.3215 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3210 Z= 0.137 Angle : 0.553 8.284 4388 Z= 0.289 Chirality : 0.040 0.162 505 Planarity : 0.004 0.031 525 Dihedral : 5.717 82.358 427 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.30 % Allowed : 22.52 % Favored : 74.17 % 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 aren not related in a simple way. whole: 2.57 (0.43), residues: 383 helix: 1.77 (0.28), residues: 326 sheet: None (None), residues: 0 loop : 1.69 (0.99), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 456 TYR 0.017 0.001 TYR A 280 PHE 0.018 0.001 PHE A 71 TRP 0.016 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3210) covalent geometry : angle 0.55258 ( 4388) hydrogen bonds : bond 0.04623 ( 247) hydrogen bonds : angle 4.05238 ( 741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.120 Fit side-chains REVERT: A 296 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8467 (mp) REVERT: A 383 TYR cc_start: 0.8784 (t80) cc_final: 0.8516 (t80) REVERT: A 384 MET cc_start: 0.8933 (mmt) cc_final: 0.8719 (mmt) REVERT: A 458 MET cc_start: 0.7561 (mmp) cc_final: 0.7354 (mmt) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 0.0494 time to fit residues: 3.3327 Evaluate side-chains 49 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 444 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3610 r_free = 0.3610 target = 0.141190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116634 restraints weight = 3401.410| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.63 r_work: 0.3208 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3210 Z= 0.149 Angle : 0.559 7.947 4388 Z= 0.292 Chirality : 0.041 0.163 505 Planarity : 0.004 0.032 525 Dihedral : 5.725 82.477 427 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.30 % Allowed : 22.22 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.43), residues: 383 helix: 1.76 (0.28), residues: 326 sheet: None (None), residues: 0 loop : 1.73 (0.99), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 402 TYR 0.016 0.001 TYR A 280 PHE 0.019 0.001 PHE A 71 TRP 0.014 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3210) covalent geometry : angle 0.55883 ( 4388) hydrogen bonds : bond 0.04682 ( 247) hydrogen bonds : angle 4.04822 ( 741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.113 Fit side-chains REVERT: A 383 TYR cc_start: 0.8852 (t80) cc_final: 0.8595 (t80) REVERT: A 384 MET cc_start: 0.8940 (mmt) cc_final: 0.8626 (mmt) REVERT: A 458 MET cc_start: 0.7599 (mmp) cc_final: 0.7392 (mmt) outliers start: 11 outliers final: 9 residues processed: 50 average time/residue: 0.0496 time to fit residues: 3.2651 Evaluate side-chains 49 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 444 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.0670 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3647 r_free = 0.3647 target = 0.143081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.118625 restraints weight = 3417.878| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.60 r_work: 0.3235 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3210 Z= 0.145 Angle : 0.562 7.616 4388 Z= 0.291 Chirality : 0.041 0.163 505 Planarity : 0.004 0.032 525 Dihedral : 5.719 82.621 427 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.30 % Allowed : 22.52 % Favored : 74.17 % 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 aren not related in a simple way. whole: 2.61 (0.43), residues: 383 helix: 1.79 (0.28), residues: 326 sheet: None (None), residues: 0 loop : 1.75 (0.99), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 402 TYR 0.016 0.001 TYR A 280 PHE 0.019 0.001 PHE A 71 TRP 0.015 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 3210) covalent geometry : angle 0.56177 ( 4388) hydrogen bonds : bond 0.04651 ( 247) hydrogen bonds : angle 4.03170 ( 741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.113 Fit side-chains REVERT: A 296 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8476 (mp) REVERT: A 383 TYR cc_start: 0.8845 (t80) cc_final: 0.8590 (t80) REVERT: A 384 MET cc_start: 0.8959 (mmt) cc_final: 0.8653 (mmt) REVERT: A 458 MET cc_start: 0.7561 (mmp) cc_final: 0.7348 (mmt) outliers start: 11 outliers final: 9 residues processed: 49 average time/residue: 0.0519 time to fit residues: 3.3664 Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 457 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.0030 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3645 r_free = 0.3645 target = 0.144280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.120642 restraints weight = 3347.989| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.54 r_work: 0.3214 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3210 Z= 0.139 Angle : 0.555 7.511 4388 Z= 0.287 Chirality : 0.041 0.162 505 Planarity : 0.004 0.031 525 Dihedral : 5.723 83.285 427 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.60 % Allowed : 22.22 % Favored : 74.17 % 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 aren not related in a simple way. whole: 2.72 (0.43), residues: 383 helix: 1.87 (0.28), residues: 326 sheet: None (None), residues: 0 loop : 1.75 (0.99), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 402 TYR 0.016 0.001 TYR A 280 PHE 0.018 0.001 PHE A 71 TRP 0.015 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3210) covalent geometry : angle 0.55499 ( 4388) hydrogen bonds : bond 0.04578 ( 247) hydrogen bonds : angle 3.98449 ( 741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.125 Fit side-chains REVERT: A 296 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8395 (mp) REVERT: A 383 TYR cc_start: 0.8807 (t80) cc_final: 0.8580 (t80) REVERT: A 384 MET cc_start: 0.8929 (mmt) cc_final: 0.8699 (mmt) REVERT: A 458 MET cc_start: 0.7506 (mmp) cc_final: 0.7303 (mmt) outliers start: 12 outliers final: 11 residues processed: 51 average time/residue: 0.0515 time to fit residues: 3.4884 Evaluate side-chains 52 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 457 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 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 = 0.3651 r_free = 0.3651 target = 0.143696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119232 restraints weight = 3427.514| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.62 r_work: 0.3242 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3210 Z= 0.144 Angle : 0.567 7.872 4388 Z= 0.292 Chirality : 0.041 0.162 505 Planarity : 0.004 0.031 525 Dihedral : 5.749 83.783 427 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.60 % Allowed : 22.52 % Favored : 73.87 % 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 aren not related in a simple way. whole: 2.74 (0.43), residues: 383 helix: 1.90 (0.28), residues: 323 sheet: None (None), residues: 0 loop : 1.68 (0.95), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 402 TYR 0.016 0.001 TYR A 280 PHE 0.018 0.001 PHE A 71 TRP 0.015 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3210) covalent geometry : angle 0.56710 ( 4388) hydrogen bonds : bond 0.04614 ( 247) hydrogen bonds : angle 4.00052 ( 741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 949.66 seconds wall clock time: 17 minutes 0.38 seconds (1020.38 seconds total)