Starting phenix.real_space_refine on Wed Jul 1 21:45:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ll0_63190/07_2026/9ll0_63190.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ll0_63190/07_2026/9ll0_63190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ll0_63190/07_2026/9ll0_63190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ll0_63190/07_2026/9ll0_63190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ll0_63190/07_2026/9ll0_63190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ll0_63190/07_2026/9ll0_63190.map" } resolution = 3.28 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= 0.000 sd= 0.047 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 19 5.16 5 C 2020 2.51 5 N 486 2.21 5 O 543 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3069 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3053 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 15, 'TRANS': 383} Chain breaks: 2 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'BG6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.95, per 1000 atoms: 0.31 Number of scatterers: 3069 At special positions: 0 Unit cell: (74.8, 60.35, 70.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 1 15.00 O 543 8.00 N 486 7.00 C 2020 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: 0.25 Conformation dependent library (CDL) restraints added in 122.9 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 718 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 82.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 8 through 42 Proline residue: A 36 - end of helix Processing helix chain 'A' and resid 47 through 70 Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.760A pdb=" N TRP A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.566A pdb=" N ASN A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.508A pdb=" N LEU A 125 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 removed outlier: 3.551A pdb=" N ALA A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.592A pdb=" N THR A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.641A pdb=" N THR A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 225 through 253 removed outlier: 3.572A pdb=" N GLY A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLN A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 286 removed outlier: 3.555A pdb=" N GLY A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N TYR A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 286 " --> pdb=" O TYR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 321 Processing helix chain 'A' and resid 327 through 356 removed outlier: 3.892A pdb=" N ILE A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Proline residue: A 345 - end of helix removed outlier: 3.604A pdb=" N ASN A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 380 removed outlier: 4.170A pdb=" N ILE A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 392 through 414 removed outlier: 3.564A pdb=" N ALA A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 663 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: 0.43 Time building geometry restraints manager: 0.35 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: 782 1.34 - 1.45: 682 1.45 - 1.57: 1659 1.57 - 1.69: 1 1.69 - 1.81: 31 Bond restraints: 3155 Sorted by residual: bond pdb=" O6 BG6 A 501 " pdb=" P BG6 A 501 " ideal model delta sigma weight residual 1.723 1.644 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" N MET A 311 " pdb=" CA MET A 311 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.23e-02 6.61e+03 1.33e+01 bond pdb=" N ASP A 47 " pdb=" CA ASP A 47 " ideal model delta sigma weight residual 1.455 1.492 -0.038 1.37e-02 5.33e+03 7.58e+00 bond pdb=" N ASP A 285 " pdb=" CA ASP A 285 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.18e+00 bond pdb=" N TRP A 107 " pdb=" CA TRP A 107 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.14e+00 ... (remaining 3150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 4131 1.73 - 3.46: 122 3.46 - 5.19: 32 5.19 - 6.92: 7 6.92 - 8.64: 4 Bond angle restraints: 4296 Sorted by residual: angle pdb=" C LEU A 234 " pdb=" N VAL A 235 " pdb=" CA VAL A 235 " ideal model delta sigma weight residual 121.65 115.81 5.84 1.48e+00 4.57e-01 1.55e+01 angle pdb=" N VAL A 235 " pdb=" CA VAL A 235 " pdb=" C VAL A 235 " ideal model delta sigma weight residual 111.45 107.91 3.54 9.30e-01 1.16e+00 1.45e+01 angle pdb=" CA PHE A 108 " pdb=" CB PHE A 108 " pdb=" CG PHE A 108 " ideal model delta sigma weight residual 113.80 117.40 -3.60 1.00e+00 1.00e+00 1.30e+01 angle pdb=" N TRP A 107 " pdb=" CA TRP A 107 " pdb=" C TRP A 107 " ideal model delta sigma weight residual 113.50 109.17 4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" C PHE A 108 " pdb=" CA PHE A 108 " pdb=" CB PHE A 108 " ideal model delta sigma weight residual 109.99 102.90 7.09 2.09e+00 2.29e-01 1.15e+01 ... (remaining 4291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.84: 1445 11.84 - 23.68: 185 23.68 - 35.52: 118 35.52 - 47.36: 32 47.36 - 59.20: 20 Dihedral angle restraints: 1800 sinusoidal: 670 harmonic: 1130 Sorted by residual: dihedral pdb=" CA THR A 30 " pdb=" C THR A 30 " pdb=" N PHE A 31 " pdb=" CA PHE A 31 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" C PHE A 108 " pdb=" N PHE A 108 " pdb=" CA PHE A 108 " pdb=" CB PHE A 108 " ideal model delta harmonic sigma weight residual -122.60 -114.84 -7.76 0 2.50e+00 1.60e-01 9.64e+00 dihedral pdb=" CB MET A 17 " pdb=" CG MET A 17 " pdb=" SD MET A 17 " pdb=" CE MET A 17 " ideal model delta sinusoidal sigma weight residual -180.00 -122.14 -57.86 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 1797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 344 0.037 - 0.075: 108 0.075 - 0.112: 26 0.112 - 0.149: 8 0.149 - 0.187: 2 Chirality restraints: 488 Sorted by residual: chirality pdb=" CA MET A 311 " pdb=" N MET A 311 " pdb=" C MET A 311 " pdb=" CB MET A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA LEU A 109 " pdb=" N LEU A 109 " pdb=" C LEU A 109 " pdb=" CB LEU A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA PHE A 108 " pdb=" N PHE A 108 " pdb=" C PHE A 108 " pdb=" CB PHE A 108 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 485 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 108 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.84e+00 pdb=" C PHE A 108 " -0.045 2.00e-02 2.50e+03 pdb=" O PHE A 108 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 109 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 8 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C TYR A 8 " -0.045 2.00e-02 2.50e+03 pdb=" O TYR A 8 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR A 9 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 233 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C TYR A 233 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR A 233 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 234 " 0.014 2.00e-02 2.50e+03 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 979 2.82 - 3.34: 2926 3.34 - 3.86: 4939 3.86 - 4.38: 5233 4.38 - 4.90: 9626 Nonbonded interactions: 23703 Sorted by model distance: nonbonded pdb=" OE1 GLU A 41 " pdb=" NE1 TRP A 165 " model vdw 2.305 3.120 nonbonded pdb=" O LEU A 317 " pdb=" OG1 THR A 321 " model vdw 2.326 3.040 nonbonded pdb=" N ASN A 189 " pdb=" OD1 ASN A 189 " model vdw 2.421 3.120 nonbonded pdb=" OG SER A 356 " pdb=" O THR A 419 " model vdw 2.442 3.040 nonbonded pdb=" OG SER A 54 " pdb=" N LEU A 382 " model vdw 2.445 3.120 ... (remaining 23698 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: 1.070 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.840 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: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 0.079 3155 Z= 0.255 Angle : 0.748 8.644 4296 Z= 0.430 Chirality : 0.041 0.187 488 Planarity : 0.005 0.050 522 Dihedral : 16.156 59.201 1082 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.31 % Allowed : 28.26 % Favored : 71.43 % 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: 1.55 (0.45), residues: 393 helix: 1.79 (0.31), residues: 311 sheet: None (None), residues: 0 loop : -2.03 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.014 0.001 TYR A 24 PHE 0.023 0.002 PHE A 33 TRP 0.016 0.001 TRP A 107 HIS 0.002 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.25 ( 3155) covalent geometry : angle 0.74774 / 0.43 ( 4296) hydrogen bonds : bond 0.12099 / 7.55 ( 221) hydrogen bonds : angle 4.68634 / 3.35 ( 663) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.105 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.0514 time to fit residues: 2.2629 Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.177983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.152608 restraints weight = 3758.051| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.75 r_work: 0.3503 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3155 Z= 0.140 Angle : 0.551 6.232 4296 Z= 0.297 Chirality : 0.037 0.141 488 Planarity : 0.005 0.036 522 Dihedral : 6.094 59.464 453 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.11 % Allowed : 26.40 % Favored : 70.50 % 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: 1.77 (0.45), residues: 393 helix: 1.96 (0.31), residues: 311 sheet: None (None), residues: 0 loop : -2.01 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 286 TYR 0.014 0.001 TYR A 24 PHE 0.022 0.001 PHE A 33 TRP 0.014 0.001 TRP A 107 HIS 0.002 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 3155) covalent geometry : angle 0.55057 / 0.30 ( 4296) hydrogen bonds : bond 0.05845 / 3.87 ( 221) hydrogen bonds : angle 3.55477 / 2.52 ( 663) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.071 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 43 average time/residue: 0.0279 time to fit residues: 1.6493 Evaluate side-chains 39 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 392 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.175377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149030 restraints weight = 3769.936| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.78 r_work: 0.3479 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3155 Z= 0.156 Angle : 0.565 5.884 4296 Z= 0.306 Chirality : 0.038 0.139 488 Planarity : 0.005 0.036 522 Dihedral : 5.927 59.057 450 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.73 % Allowed : 28.57 % Favored : 67.70 % 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: 1.91 (0.45), residues: 393 helix: 2.05 (0.31), residues: 310 sheet: None (None), residues: 0 loop : -1.87 (0.66), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 286 TYR 0.015 0.001 TYR A 24 PHE 0.021 0.002 PHE A 33 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 3155) covalent geometry : angle 0.56495 / 0.31 ( 4296) hydrogen bonds : bond 0.06256 / 4.14 ( 221) hydrogen bonds : angle 3.57916 / 2.53 ( 663) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.105 Fit side-chains REVERT: A 8 TYR cc_start: 0.4755 (OUTLIER) cc_final: 0.3810 (m-80) REVERT: A 171 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6478 (tt) REVERT: A 415 ARG cc_start: 0.6141 (mtm110) cc_final: 0.5850 (ttm110) outliers start: 12 outliers final: 8 residues processed: 43 average time/residue: 0.0435 time to fit residues: 2.5391 Evaluate side-chains 44 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 TYR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.0040 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.178364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.152199 restraints weight = 3757.698| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.80 r_work: 0.3510 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3155 Z= 0.132 Angle : 0.528 6.067 4296 Z= 0.284 Chirality : 0.036 0.131 488 Planarity : 0.004 0.035 522 Dihedral : 5.720 57.565 450 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.73 % Allowed : 30.43 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.16 (0.45), residues: 393 helix: 2.22 (0.31), residues: 309 sheet: None (None), residues: 0 loop : -1.72 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 10 TYR 0.014 0.001 TYR A 24 PHE 0.019 0.001 PHE A 33 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 3155) covalent geometry : angle 0.52762 / 0.28 ( 4296) hydrogen bonds : bond 0.05572 / 3.74 ( 221) hydrogen bonds : angle 3.49001 / 2.46 ( 663) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.132 Fit side-chains REVERT: A 8 TYR cc_start: 0.4804 (OUTLIER) cc_final: 0.3849 (m-80) REVERT: A 171 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6414 (tt) REVERT: A 415 ARG cc_start: 0.6201 (mtm110) cc_final: 0.5844 (ttm110) outliers start: 12 outliers final: 6 residues processed: 44 average time/residue: 0.0411 time to fit residues: 2.4562 Evaluate side-chains 43 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 TYR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 413 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.0070 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.170488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143606 restraints weight = 3747.056| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.78 r_work: 0.3491 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3155 Z= 0.136 Angle : 0.539 6.502 4296 Z= 0.290 Chirality : 0.037 0.131 488 Planarity : 0.004 0.036 522 Dihedral : 5.596 56.265 450 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.28 % Allowed : 29.19 % Favored : 65.53 % 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: 2.17 (0.45), residues: 393 helix: 2.24 (0.31), residues: 309 sheet: None (None), residues: 0 loop : -1.76 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 286 TYR 0.014 0.001 TYR A 24 PHE 0.019 0.001 PHE A 33 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 3155) covalent geometry : angle 0.53888 / 0.29 ( 4296) hydrogen bonds : bond 0.05684 / 3.80 ( 221) hydrogen bonds : angle 3.47182 / 2.44 ( 663) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.106 Fit side-chains REVERT: A 8 TYR cc_start: 0.4707 (OUTLIER) cc_final: 0.3810 (m-80) REVERT: A 171 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6427 (tt) REVERT: A 415 ARG cc_start: 0.6156 (mtm110) cc_final: 0.5773 (ttm110) outliers start: 17 outliers final: 8 residues processed: 47 average time/residue: 0.0422 time to fit residues: 2.6927 Evaluate side-chains 45 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 TYR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 413 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.171615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.146615 restraints weight = 3745.186| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.62 r_work: 0.3423 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3155 Z= 0.190 Angle : 0.614 6.276 4296 Z= 0.333 Chirality : 0.040 0.140 488 Planarity : 0.005 0.038 522 Dihedral : 5.654 54.878 450 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.59 % Allowed : 28.57 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.81 (0.44), residues: 393 helix: 1.98 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -1.86 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 286 TYR 0.016 0.001 TYR A 24 PHE 0.020 0.002 PHE A 33 TRP 0.012 0.002 TRP A 107 HIS 0.001 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 3155) covalent geometry : angle 0.61379 / 0.33 ( 4296) hydrogen bonds : bond 0.07070 / 4.65 ( 221) hydrogen bonds : angle 3.77239 / 2.67 ( 663) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.066 Fit side-chains REVERT: A 8 TYR cc_start: 0.5018 (OUTLIER) cc_final: 0.3850 (m-80) REVERT: A 171 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6657 (tt) REVERT: A 415 ARG cc_start: 0.6215 (mtm110) cc_final: 0.5788 (ttm110) outliers start: 18 outliers final: 11 residues processed: 47 average time/residue: 0.0343 time to fit residues: 2.1846 Evaluate side-chains 46 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 TYR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 413 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.177143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.150703 restraints weight = 3774.108| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.81 r_work: 0.3491 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3155 Z= 0.137 Angle : 0.550 6.630 4296 Z= 0.294 Chirality : 0.037 0.129 488 Planarity : 0.004 0.035 522 Dihedral : 5.418 53.139 450 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.97 % Allowed : 30.12 % Favored : 64.91 % 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: 2.05 (0.44), residues: 393 helix: 2.15 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -1.80 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 10 TYR 0.013 0.001 TYR A 8 PHE 0.018 0.001 PHE A 33 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 3155) covalent geometry : angle 0.54962 / 0.29 ( 4296) hydrogen bonds : bond 0.05726 / 3.85 ( 221) hydrogen bonds : angle 3.54029 / 2.50 ( 663) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.106 Fit side-chains REVERT: A 8 TYR cc_start: 0.4956 (OUTLIER) cc_final: 0.3980 (m-80) REVERT: A 171 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6473 (tt) REVERT: A 415 ARG cc_start: 0.6157 (mtm110) cc_final: 0.5690 (ttm110) outliers start: 16 outliers final: 10 residues processed: 47 average time/residue: 0.0326 time to fit residues: 2.1146 Evaluate side-chains 47 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 TYR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 413 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.0020 chunk 26 optimal weight: 0.0670 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.184439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.158335 restraints weight = 3813.693| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.90 r_work: 0.3520 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3155 Z= 0.121 Angle : 0.526 7.589 4296 Z= 0.278 Chirality : 0.036 0.132 488 Planarity : 0.004 0.035 522 Dihedral : 5.112 49.913 450 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.04 % Allowed : 31.37 % Favored : 64.60 % 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: 2.26 (0.45), residues: 393 helix: 2.32 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -1.77 (0.65), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 10 TYR 0.013 0.001 TYR A 24 PHE 0.017 0.001 PHE A 33 TRP 0.013 0.001 TRP A 107 HIS 0.002 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 3155) covalent geometry : angle 0.52568 / 0.28 ( 4296) hydrogen bonds : bond 0.05065 / 3.43 ( 221) hydrogen bonds : angle 3.38062 / 2.38 ( 663) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.102 Fit side-chains REVERT: A 8 TYR cc_start: 0.4540 (OUTLIER) cc_final: 0.3712 (m-80) REVERT: A 171 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6399 (tt) REVERT: A 415 ARG cc_start: 0.6169 (mtm110) cc_final: 0.5671 (ttm110) outliers start: 13 outliers final: 8 residues processed: 47 average time/residue: 0.0341 time to fit residues: 2.1976 Evaluate side-chains 48 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 TYR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 413 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.0010 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.182217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.156891 restraints weight = 3859.377| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.83 r_work: 0.3549 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3155 Z= 0.119 Angle : 0.540 8.112 4296 Z= 0.280 Chirality : 0.036 0.133 488 Planarity : 0.004 0.036 522 Dihedral : 4.924 47.317 450 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.11 % Allowed : 31.68 % Favored : 65.22 % 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: 2.35 (0.45), residues: 393 helix: 2.36 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -1.68 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 300 TYR 0.013 0.001 TYR A 24 PHE 0.017 0.001 PHE A 33 TRP 0.013 0.001 TRP A 107 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 3155) covalent geometry : angle 0.54015 / 0.28 ( 4296) hydrogen bonds : bond 0.04917 / 3.31 ( 221) hydrogen bonds : angle 3.35112 / 2.36 ( 663) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.081 Fit side-chains REVERT: A 8 TYR cc_start: 0.4472 (OUTLIER) cc_final: 0.3717 (m-80) REVERT: A 171 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6362 (tt) REVERT: A 415 ARG cc_start: 0.6104 (mtm110) cc_final: 0.5618 (ttm110) outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 0.0373 time to fit residues: 2.3095 Evaluate side-chains 47 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 TYR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 413 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.167578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140960 restraints weight = 3712.391| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.77 r_work: 0.3485 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3155 Z= 0.137 Angle : 0.573 7.465 4296 Z= 0.299 Chirality : 0.038 0.130 488 Planarity : 0.004 0.037 522 Dihedral : 4.879 45.609 450 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.11 % Allowed : 31.99 % Favored : 64.91 % 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: 2.25 (0.44), residues: 393 helix: 2.28 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -1.66 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 28 TYR 0.015 0.001 TYR A 24 PHE 0.033 0.002 PHE A 33 TRP 0.011 0.001 TRP A 107 HIS 0.002 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 3155) covalent geometry : angle 0.57254 / 0.30 ( 4296) hydrogen bonds : bond 0.05571 / 3.71 ( 221) hydrogen bonds : angle 3.46783 / 2.45 ( 663) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.082 Fit side-chains REVERT: A 8 TYR cc_start: 0.4527 (OUTLIER) cc_final: 0.3753 (m-80) REVERT: A 171 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6426 (tt) REVERT: A 415 ARG cc_start: 0.6099 (mtm110) cc_final: 0.5602 (ttm110) outliers start: 10 outliers final: 6 residues processed: 45 average time/residue: 0.0436 time to fit residues: 2.6437 Evaluate side-chains 46 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 TYR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 413 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.168355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.141335 restraints weight = 3820.924| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.81 r_work: 0.3476 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3155 Z= 0.140 Angle : 0.571 7.762 4296 Z= 0.299 Chirality : 0.038 0.131 488 Planarity : 0.004 0.037 522 Dihedral : 4.790 43.698 450 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.48 % Allowed : 32.30 % Favored : 65.22 % 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: 2.22 (0.44), residues: 393 helix: 2.25 (0.30), residues: 309 sheet: None (None), residues: 0 loop : -1.62 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 10 TYR 0.014 0.001 TYR A 24 PHE 0.034 0.002 PHE A 33 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 3155) covalent geometry : angle 0.57077 / 0.30 ( 4296) hydrogen bonds : bond 0.05679 / 3.79 ( 221) hydrogen bonds : angle 3.50305 / 2.47 ( 663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 820.12 seconds wall clock time: 14 minutes 44.41 seconds (884.41 seconds total)