Starting phenix.real_space_refine on Fri May 9 13:23:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kig_37259/05_2025/8kig_37259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kig_37259/05_2025/8kig_37259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kig_37259/05_2025/8kig_37259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kig_37259/05_2025/8kig_37259.map" model { file = "/net/cci-nas-00/data/ceres_data/8kig_37259/05_2025/8kig_37259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kig_37259/05_2025/8kig_37259.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 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 Ca 1 9.91 5 S 27 5.16 5 C 1405 2.51 5 N 327 2.21 5 O 344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2104 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2025 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'4J2:plan-2': 1, 'NLE:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.32, per 1000 atoms: 1.10 Number of scatterers: 2104 At special positions: 0 Unit cell: (74.8, 64.6, 79.05, 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) Ca 1 19.99 S 27 16.00 O 344 8.00 N 327 7.00 C 1405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 268 " - pdb=" SG CYS R 274 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 236.9 milliseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 4J2 L 4 " Number of C-beta restraints generated: 514 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 83.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 41 through 66 removed outlier: 4.125A pdb=" N PHE R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 103 removed outlier: 3.522A pdb=" N ALA R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 121 removed outlier: 3.752A pdb=" N ASN R 118 " --> pdb=" O GLN R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 148 removed outlier: 3.680A pdb=" N VAL R 129 " --> pdb=" O CYS R 125 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER R 131 " --> pdb=" O SER R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 156 Processing helix chain 'R' and resid 157 through 182 removed outlier: 3.794A pdb=" N ILE R 180 " --> pdb=" O GLY R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 211 removed outlier: 3.505A pdb=" N VAL R 190 " --> pdb=" O LYS R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 241 removed outlier: 4.053A pdb=" N ALA R 241 " --> pdb=" O CYS R 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 237 through 241' Processing helix chain 'R' and resid 242 through 265 removed outlier: 3.526A pdb=" N PHE R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE R 252 " --> pdb=" O LEU R 248 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE R 253 " --> pdb=" O GLY R 249 " (cutoff:3.500A) Proline residue: R 257 - end of helix removed outlier: 3.565A pdb=" N HIS R 261 " --> pdb=" O PRO R 257 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU R 262 " --> pdb=" O PHE R 258 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE R 265 " --> pdb=" O HIS R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 279 removed outlier: 3.845A pdb=" N CYS R 276 " --> pdb=" O PRO R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 Processing helix chain 'R' and resid 285 through 291 Processing helix chain 'R' and resid 294 through 301 Processing helix chain 'R' and resid 303 through 315 removed outlier: 3.627A pdb=" N ARG R 307 " --> pdb=" O SER R 303 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 432 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: 0.50 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 604 1.34 - 1.46: 406 1.46 - 1.58: 1101 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 2151 Sorted by residual: bond pdb=" CA 4J2 L 4 " pdb=" C 4J2 L 4 " ideal model delta sigma weight residual 1.525 1.561 -0.036 2.10e-02 2.27e+03 2.98e+00 bond pdb=" CG PRO R 72 " pdb=" CD PRO R 72 " ideal model delta sigma weight residual 1.503 1.556 -0.053 3.40e-02 8.65e+02 2.46e+00 bond pdb=" C TYR R 74 " pdb=" O TYR R 74 " ideal model delta sigma weight residual 1.235 1.215 0.021 1.33e-02 5.65e+03 2.39e+00 bond pdb=" N TYR R 74 " pdb=" CA TYR R 74 " ideal model delta sigma weight residual 1.456 1.475 -0.019 1.32e-02 5.74e+03 2.08e+00 bond pdb=" CB 4J2 L 4 " pdb=" CG 4J2 L 4 " ideal model delta sigma weight residual 1.501 1.472 0.029 2.00e-02 2.50e+03 2.06e+00 ... (remaining 2146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 2795 1.46 - 2.92: 101 2.92 - 4.37: 22 4.37 - 5.83: 5 5.83 - 7.29: 3 Bond angle restraints: 2926 Sorted by residual: angle pdb=" CA TYR R 105 " pdb=" C TYR R 105 " pdb=" N LEU R 106 " ideal model delta sigma weight residual 118.22 121.03 -2.81 1.03e+00 9.43e-01 7.46e+00 angle pdb=" CB MET R 289 " pdb=" CG MET R 289 " pdb=" SD MET R 289 " ideal model delta sigma weight residual 112.70 105.60 7.10 3.00e+00 1.11e-01 5.60e+00 angle pdb=" C THR R 107 " pdb=" N PHE R 108 " pdb=" CA PHE R 108 " ideal model delta sigma weight residual 122.50 118.53 3.97 1.82e+00 3.02e-01 4.76e+00 angle pdb=" N VAL R 263 " pdb=" CA VAL R 263 " pdb=" C VAL R 263 " ideal model delta sigma weight residual 113.16 109.94 3.22 1.49e+00 4.50e-01 4.66e+00 angle pdb=" CA LEU R 106 " pdb=" CB LEU R 106 " pdb=" CG LEU R 106 " ideal model delta sigma weight residual 116.30 123.59 -7.29 3.50e+00 8.16e-02 4.34e+00 ... (remaining 2921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 1047 16.43 - 32.86: 159 32.86 - 49.30: 38 49.30 - 65.73: 8 65.73 - 82.16: 2 Dihedral angle restraints: 1254 sinusoidal: 468 harmonic: 786 Sorted by residual: dihedral pdb=" CA GLU R 109 " pdb=" C GLU R 109 " pdb=" N ASP R 110 " pdb=" CA ASP R 110 " ideal model delta harmonic sigma weight residual -180.00 -154.24 -25.76 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA LEU R 262 " pdb=" C LEU R 262 " pdb=" N VAL R 263 " pdb=" CA VAL R 263 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CB CYS R 268 " pdb=" SG CYS R 268 " pdb=" SG CYS R 274 " pdb=" CB CYS R 274 " ideal model delta sinusoidal sigma weight residual -86.00 -122.89 36.89 1 1.00e+01 1.00e-02 1.92e+01 ... (remaining 1251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 196 0.033 - 0.065: 126 0.065 - 0.098: 28 0.098 - 0.131: 7 0.131 - 0.163: 7 Chirality restraints: 364 Sorted by residual: chirality pdb=" CG LEU R 106 " pdb=" CB LEU R 106 " pdb=" CD1 LEU R 106 " pdb=" CD2 LEU R 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CB THR R 194 " pdb=" CA THR R 194 " pdb=" OG1 THR R 194 " pdb=" CG2 THR R 194 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA PRO R 72 " pdb=" N PRO R 72 " pdb=" C PRO R 72 " pdb=" CB PRO R 72 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 361 not shown) Planarity restraints: 344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 71 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO R 72 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO R 72 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 72 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 302 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C ARG R 302 " 0.020 2.00e-02 2.50e+03 pdb=" O ARG R 302 " -0.007 2.00e-02 2.50e+03 pdb=" N SER R 303 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 197 " -0.009 2.00e-02 2.50e+03 6.30e-03 6.95e-01 pdb=" CG PHE R 197 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE R 197 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 197 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 197 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE R 197 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 197 " -0.001 2.00e-02 2.50e+03 ... (remaining 341 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 62 2.69 - 3.24: 2154 3.24 - 3.80: 3228 3.80 - 4.35: 4073 4.35 - 4.90: 6765 Nonbonded interactions: 16282 Sorted by model distance: nonbonded pdb=" O VAL R 263 " pdb=" OG1 THR R 267 " model vdw 2.138 3.040 nonbonded pdb=" OG SER R 52 " pdb=" OG SER R 88 " model vdw 2.146 3.040 nonbonded pdb=" OE2 GLU R 94 " pdb="CA CA R 401 " model vdw 2.173 2.510 nonbonded pdb=" O SER R 127 " pdb=" OG SER R 127 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP R 121 " pdb="CA CA R 401 " model vdw 2.262 2.510 ... (remaining 16277 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.380 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.007 0.102 2153 Z= 0.354 Angle : 0.719 7.289 2928 Z= 0.370 Chirality : 0.046 0.163 364 Planarity : 0.005 0.066 344 Dihedral : 16.913 82.158 737 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.85 % Allowed : 37.02 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.56), residues: 255 helix: 0.14 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -1.55 (1.06), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 169 HIS 0.002 0.001 HIS R 261 PHE 0.014 0.002 PHE R 259 TYR 0.011 0.002 TYR R 152 ARG 0.007 0.001 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.20409 ( 146) hydrogen bonds : angle 7.09416 ( 432) SS BOND : bond 0.00209 ( 1) SS BOND : angle 1.04727 ( 2) covalent geometry : bond 0.00653 ( 2151) covalent geometry : angle 0.71890 ( 2926) Misc. bond : bond 0.10198 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.229 Fit side-chains REVERT: R 307 ARG cc_start: 0.8720 (mtp85) cc_final: 0.8370 (mtm-85) outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.1795 time to fit residues: 10.7851 Evaluate side-chains 51 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 145 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.161890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128078 restraints weight = 2824.822| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.73 r_work: 0.3501 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2153 Z= 0.145 Angle : 0.602 6.400 2928 Z= 0.313 Chirality : 0.041 0.151 364 Planarity : 0.003 0.018 344 Dihedral : 5.096 26.558 286 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.53 % Allowed : 29.79 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.56), residues: 255 helix: 0.81 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.65 (1.18), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 169 HIS 0.001 0.000 HIS R 153 PHE 0.018 0.001 PHE R 197 TYR 0.011 0.001 TYR R 277 ARG 0.006 0.001 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.04946 ( 146) hydrogen bonds : angle 4.82982 ( 432) SS BOND : bond 0.00309 ( 1) SS BOND : angle 0.74173 ( 2) covalent geometry : bond 0.00321 ( 2151) covalent geometry : angle 0.60224 ( 2926) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.241 Fit side-chains REVERT: R 184 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5672 (pm20) REVERT: R 197 PHE cc_start: 0.8063 (t80) cc_final: 0.7859 (t80) REVERT: R 307 ARG cc_start: 0.8693 (mtp85) cc_final: 0.8189 (mtm-85) outliers start: 13 outliers final: 3 residues processed: 62 average time/residue: 0.1403 time to fit residues: 10.1233 Evaluate side-chains 57 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.166586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133598 restraints weight = 2691.253| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.61 r_work: 0.3541 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2153 Z= 0.124 Angle : 0.545 6.079 2928 Z= 0.286 Chirality : 0.039 0.127 364 Planarity : 0.003 0.019 344 Dihedral : 4.646 25.605 285 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.68 % Allowed : 31.06 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.56), residues: 255 helix: 1.25 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.28 (1.16), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 169 HIS 0.001 0.000 HIS R 280 PHE 0.021 0.001 PHE R 197 TYR 0.009 0.001 TYR R 152 ARG 0.006 0.001 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 146) hydrogen bonds : angle 4.28309 ( 432) SS BOND : bond 0.00205 ( 1) SS BOND : angle 0.64181 ( 2) covalent geometry : bond 0.00274 ( 2151) covalent geometry : angle 0.54542 ( 2926) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.231 Fit side-chains REVERT: R 184 GLU cc_start: 0.5749 (OUTLIER) cc_final: 0.5491 (pm20) REVERT: R 307 ARG cc_start: 0.8634 (mtp85) cc_final: 0.8082 (mtm110) REVERT: R 311 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7711 (ttt90) outliers start: 11 outliers final: 4 residues processed: 60 average time/residue: 0.1473 time to fit residues: 10.2470 Evaluate side-chains 57 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.165907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.132216 restraints weight = 2730.514| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.65 r_work: 0.3539 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2153 Z= 0.132 Angle : 0.578 7.624 2928 Z= 0.292 Chirality : 0.039 0.138 364 Planarity : 0.003 0.018 344 Dihedral : 4.505 24.936 285 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.53 % Allowed : 30.64 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.57), residues: 255 helix: 1.44 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.12 (1.17), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 169 HIS 0.001 0.000 HIS R 280 PHE 0.018 0.001 PHE R 197 TYR 0.012 0.001 TYR R 277 ARG 0.006 0.001 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 146) hydrogen bonds : angle 4.11755 ( 432) SS BOND : bond 0.00272 ( 1) SS BOND : angle 0.79641 ( 2) covalent geometry : bond 0.00295 ( 2151) covalent geometry : angle 0.57751 ( 2926) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.209 Fit side-chains REVERT: R 184 GLU cc_start: 0.5789 (OUTLIER) cc_final: 0.5535 (pm20) outliers start: 13 outliers final: 7 residues processed: 63 average time/residue: 0.1362 time to fit residues: 9.9781 Evaluate side-chains 62 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.0470 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.168779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135197 restraints weight = 2708.172| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.66 r_work: 0.3579 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2153 Z= 0.108 Angle : 0.543 7.504 2928 Z= 0.273 Chirality : 0.038 0.141 364 Planarity : 0.003 0.020 344 Dihedral : 4.314 24.194 285 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.68 % Allowed : 31.91 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.57), residues: 255 helix: 1.67 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.17 (1.14), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 169 HIS 0.001 0.000 HIS R 261 PHE 0.019 0.001 PHE R 197 TYR 0.014 0.001 TYR R 277 ARG 0.007 0.001 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 146) hydrogen bonds : angle 3.92779 ( 432) SS BOND : bond 0.00065 ( 1) SS BOND : angle 0.66957 ( 2) covalent geometry : bond 0.00228 ( 2151) covalent geometry : angle 0.54340 ( 2926) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.208 Fit side-chains REVERT: R 184 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.5492 (pm20) REVERT: R 201 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8185 (mp) outliers start: 11 outliers final: 7 residues processed: 63 average time/residue: 0.1390 time to fit residues: 10.2146 Evaluate side-chains 63 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.166210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132257 restraints weight = 2720.064| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.67 r_work: 0.3540 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2153 Z= 0.135 Angle : 0.579 7.555 2928 Z= 0.289 Chirality : 0.039 0.144 364 Planarity : 0.003 0.022 344 Dihedral : 4.315 24.395 285 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 7.23 % Allowed : 30.21 % Favored : 62.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.57), residues: 255 helix: 1.72 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.20 (1.12), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 169 HIS 0.002 0.000 HIS R 261 PHE 0.011 0.001 PHE R 197 TYR 0.010 0.001 TYR R 277 ARG 0.007 0.001 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 146) hydrogen bonds : angle 3.99329 ( 432) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.93060 ( 2) covalent geometry : bond 0.00308 ( 2151) covalent geometry : angle 0.57918 ( 2926) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.224 Fit side-chains REVERT: R 184 GLU cc_start: 0.5724 (OUTLIER) cc_final: 0.5472 (pm20) REVERT: R 201 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8242 (mp) outliers start: 17 outliers final: 9 residues processed: 63 average time/residue: 0.1318 time to fit residues: 9.7787 Evaluate side-chains 62 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.167460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133435 restraints weight = 2714.874| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.68 r_work: 0.3547 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2153 Z= 0.126 Angle : 0.576 7.465 2928 Z= 0.285 Chirality : 0.039 0.148 364 Planarity : 0.003 0.024 344 Dihedral : 4.251 24.046 285 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 7.23 % Allowed : 31.06 % Favored : 61.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.57), residues: 255 helix: 1.80 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.31 (1.08), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 169 HIS 0.002 0.000 HIS R 261 PHE 0.020 0.001 PHE R 197 TYR 0.010 0.001 TYR R 277 ARG 0.006 0.001 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 146) hydrogen bonds : angle 3.93151 ( 432) SS BOND : bond 0.00199 ( 1) SS BOND : angle 0.77616 ( 2) covalent geometry : bond 0.00283 ( 2151) covalent geometry : angle 0.57621 ( 2926) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.321 Fit side-chains REVERT: R 184 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.5468 (pm20) REVERT: R 201 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8201 (mp) REVERT: R 307 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8187 (mtm-85) outliers start: 17 outliers final: 11 residues processed: 61 average time/residue: 0.1887 time to fit residues: 13.9717 Evaluate side-chains 64 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.167411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.133276 restraints weight = 2750.990| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.69 r_work: 0.3543 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2153 Z= 0.129 Angle : 0.606 8.716 2928 Z= 0.294 Chirality : 0.039 0.152 364 Planarity : 0.003 0.025 344 Dihedral : 4.241 24.032 285 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 6.38 % Allowed : 31.49 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.57), residues: 255 helix: 1.83 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.37 (1.08), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 169 HIS 0.002 0.000 HIS R 261 PHE 0.012 0.001 PHE R 197 TYR 0.010 0.001 TYR R 277 ARG 0.007 0.001 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 146) hydrogen bonds : angle 3.92038 ( 432) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.76962 ( 2) covalent geometry : bond 0.00292 ( 2151) covalent geometry : angle 0.60560 ( 2926) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.237 Fit side-chains REVERT: R 307 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8173 (mtm-85) outliers start: 15 outliers final: 11 residues processed: 57 average time/residue: 0.1256 time to fit residues: 8.4518 Evaluate side-chains 60 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 116 MET Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.134170 restraints weight = 2774.284| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.70 r_work: 0.3550 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2153 Z= 0.125 Angle : 0.604 8.234 2928 Z= 0.293 Chirality : 0.039 0.152 364 Planarity : 0.003 0.024 344 Dihedral : 4.223 23.764 285 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.53 % Allowed : 32.77 % Favored : 61.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.56), residues: 255 helix: 1.84 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.35 (1.08), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 169 HIS 0.002 0.000 HIS R 261 PHE 0.020 0.001 PHE R 197 TYR 0.010 0.001 TYR R 277 ARG 0.007 0.001 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 146) hydrogen bonds : angle 3.92892 ( 432) SS BOND : bond 0.00202 ( 1) SS BOND : angle 0.72532 ( 2) covalent geometry : bond 0.00284 ( 2151) covalent geometry : angle 0.60422 ( 2926) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.209 Fit side-chains REVERT: R 184 GLU cc_start: 0.5709 (OUTLIER) cc_final: 0.5140 (pm20) outliers start: 13 outliers final: 12 residues processed: 56 average time/residue: 0.1154 time to fit residues: 7.7486 Evaluate side-chains 61 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 116 MET Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.168627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135018 restraints weight = 2743.069| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.68 r_work: 0.3553 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2153 Z= 0.119 Angle : 0.601 8.126 2928 Z= 0.291 Chirality : 0.039 0.155 364 Planarity : 0.003 0.027 344 Dihedral : 4.173 23.524 285 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.96 % Allowed : 31.91 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.56), residues: 255 helix: 1.87 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.37 (1.07), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 169 HIS 0.001 0.000 HIS R 261 PHE 0.007 0.001 PHE R 197 TYR 0.010 0.001 TYR R 277 ARG 0.008 0.001 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 146) hydrogen bonds : angle 3.88352 ( 432) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.66870 ( 2) covalent geometry : bond 0.00264 ( 2151) covalent geometry : angle 0.60067 ( 2926) Misc. bond : bond 0.00006 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.221 Fit side-chains REVERT: R 184 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.5033 (pm20) outliers start: 14 outliers final: 12 residues processed: 58 average time/residue: 0.1188 time to fit residues: 8.2658 Evaluate side-chains 62 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 SER Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 116 MET Chi-restraints excluded: chain R residue 175 CYS Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.169219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135573 restraints weight = 2719.324| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.67 r_work: 0.3549 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2153 Z= 0.114 Angle : 0.591 7.983 2928 Z= 0.286 Chirality : 0.039 0.154 364 Planarity : 0.003 0.026 344 Dihedral : 4.115 22.990 285 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.53 % Allowed : 31.91 % Favored : 62.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.56), residues: 255 helix: 1.89 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.34 (1.07), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 169 HIS 0.001 0.000 HIS R 261 PHE 0.020 0.001 PHE R 197 TYR 0.010 0.001 TYR R 277 ARG 0.008 0.001 ARG R 302 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 146) hydrogen bonds : angle 3.84831 ( 432) SS BOND : bond 0.00189 ( 1) SS BOND : angle 0.62030 ( 2) covalent geometry : bond 0.00251 ( 2151) covalent geometry : angle 0.59093 ( 2926) Misc. bond : bond 0.00006 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1459.17 seconds wall clock time: 26 minutes 17.53 seconds (1577.53 seconds total)