Starting phenix.real_space_refine on Wed Mar 5 14:54:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kig_37259/03_2025/8kig_37259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kig_37259/03_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_37259/03_2025/8kig_37259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kig_37259/03_2025/8kig_37259.map" model { file = "/net/cci-nas-00/data/ceres_data/8kig_37259/03_2025/8kig_37259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kig_37259/03_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-5624/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: 2.88, per 1000 atoms: 1.37 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: 0.80 Conformation dependent library (CDL) restraints added in 261.5 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: 0.24 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: 0.53 Time building geometry restraints manager: 0.89 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.150 Find NCS groups from input model: 0.020 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- 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 0.053 2151 Z= 0.422 Angle : 0.719 7.289 2926 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 *********************** 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 : 0.280 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: 0.1827 time to fit residues: 11.0379 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 : 0.256 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128084 restraints weight = 2824.822| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.73 r_work: 0.3501 rms_B_bonded: 3.68 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 2151 Z= 0.207 Angle : 0.602 6.400 2926 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 *********************** 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 : 0.230 Fit side-chains REVERT: R 184 GLU cc_start: 0.5907 (OUTLIER) cc_final: 0.5670 (pm20) REVERT: R 197 PHE cc_start: 0.8064 (t80) cc_final: 0.7860 (t80) REVERT: R 307 ARG cc_start: 0.8694 (mtp85) cc_final: 0.8191 (mtm-85) outliers start: 13 outliers final: 3 residues processed: 62 average time/residue: 0.1434 time to fit residues: 10.3371 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 : 0.222 ------------------------------------------------------------------------------- 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: 0.9980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.166175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132887 restraints weight = 2699.984| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.63 r_work: 0.3533 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2151 Z= 0.184 Angle : 0.553 6.074 2926 Z= 0.290 Chirality : 0.039 0.129 364 Planarity : 0.003 0.017 344 Dihedral : 4.652 25.643 285 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.38 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: 1.43 (0.56), residues: 255 helix: 1.24 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -0.29 (1.16), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 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 0.005 0.001 ARG R 302 *********************** 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 66 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.242 Fit side-chains REVERT: R 184 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5441 (pm20) REVERT: R 197 PHE cc_start: 0.8023 (t80) cc_final: 0.7789 (t80) REVERT: R 201 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8194 (mp) REVERT: R 307 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8089 (mtm-85) REVERT: R 311 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7714 (ttt90) outliers start: 11 outliers final: 5 residues processed: 61 average time/residue: 0.1501 time to fit residues: 10.7010 Evaluate side-chains 61 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 188 VAL Chi-restraints excluded: chain R residue 201 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 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 = 0.4050 r_free = 0.4050 target = 0.165969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132381 restraints weight = 2733.568| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.66 r_work: 0.3529 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2151 Z= 0.190 Angle : 0.573 6.034 2926 Z= 0.294 Chirality : 0.039 0.136 364 Planarity : 0.003 0.018 344 Dihedral : 4.525 25.011 285 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.96 % Allowed : 29.79 % 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: 1.70 (0.57), residues: 255 helix: 1.41 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.13 (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 0.021 0.001 PHE R 197 TYR 0.008 0.001 TYR R 277 ARG 0.006 0.001 ARG R 302 *********************** 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 70 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.250 Fit side-chains REVERT: R 184 GLU cc_start: 0.5751 (OUTLIER) cc_final: 0.5498 (pm20) REVERT: R 201 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8211 (mp) outliers start: 14 outliers final: 6 residues processed: 64 average time/residue: 0.1430 time to fit residues: 10.6548 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 : 0.223 ------------------------------------------------------------------------------- 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 201 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: 0.7980 chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 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: 0.5780 ------------------------------------------------------------------------------- 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 = 0.168308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134770 restraints weight = 2713.234| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.66 r_work: 0.3572 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2151 Z= 0.156 Angle : 0.553 7.938 2926 Z= 0.278 Chirality : 0.038 0.141 364 Planarity : 0.003 0.019 344 Dihedral : 4.350 24.312 285 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: 2.02 (0.57), residues: 255 helix: 1.65 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.21 (1.15), 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 0.017 0.001 PHE R 197 TYR 0.016 0.001 TYR R 277 ARG 0.007 0.001 ARG R 302 *********************** 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 69 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.236 Fit side-chains REVERT: R 184 GLU cc_start: 0.5744 (OUTLIER) cc_final: 0.5479 (pm20) REVERT: R 201 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8212 (mp) outliers start: 13 outliers final: 7 residues processed: 63 average time/residue: 0.1469 time to fit residues: 10.7414 Evaluate side-chains 62 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=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: 0.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.165674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131904 restraints weight = 2719.241| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.66 r_work: 0.3530 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2151 Z= 0.202 Angle : 0.585 7.920 2926 Z= 0.292 Chirality : 0.039 0.145 364 Planarity : 0.003 0.023 344 Dihedral : 4.353 24.440 285 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 7.66 % Allowed : 29.36 % Favored : 62.98 % 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: 2.08 (0.57), residues: 255 helix: 1.70 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.24 (1.13), 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 0.013 0.001 TYR R 277 ARG 0.007 0.001 ARG R 302 *********************** 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 70 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.227 Fit side-chains REVERT: R 184 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.5471 (pm20) REVERT: R 201 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8281 (mp) REVERT: R 307 ARG cc_start: 0.8669 (mtp85) cc_final: 0.8216 (mtm-85) outliers start: 18 outliers final: 11 residues processed: 62 average time/residue: 0.1353 time to fit residues: 9.8718 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 : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 58 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.166494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132376 restraints weight = 2719.835| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.68 r_work: 0.3535 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2151 Z= 0.199 Angle : 0.592 7.931 2926 Z= 0.293 Chirality : 0.039 0.148 364 Planarity : 0.003 0.024 344 Dihedral : 4.336 24.254 285 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 6.81 % Allowed : 30.21 % Favored : 62.98 % 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: 2.10 (0.57), residues: 255 helix: 1.73 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.36 (1.09), 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 0.013 0.001 PHE R 197 TYR 0.012 0.001 TYR R 277 ARG 0.007 0.001 ARG R 302 *********************** 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 67 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.240 Fit side-chains REVERT: R 184 GLU cc_start: 0.5734 (OUTLIER) cc_final: 0.5453 (pm20) REVERT: R 307 ARG cc_start: 0.8645 (mtp85) cc_final: 0.8187 (mtm-85) outliers start: 16 outliers final: 12 residues processed: 60 average time/residue: 0.1366 time to fit residues: 9.6474 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 : 0.234 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.169649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135667 restraints weight = 2739.953| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.69 r_work: 0.3579 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2151 Z= 0.149 Angle : 0.586 8.407 2926 Z= 0.284 Chirality : 0.038 0.146 364 Planarity : 0.003 0.025 344 Dihedral : 4.198 23.562 285 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.38 % Allowed : 31.06 % 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: 2.29 (0.56), residues: 255 helix: 1.87 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.33 (1.07), 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 0.021 0.001 PHE R 197 TYR 0.011 0.001 TYR R 277 ARG 0.007 0.001 ARG R 302 *********************** 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 65 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.212 Fit side-chains REVERT: R 184 GLU cc_start: 0.5708 (OUTLIER) cc_final: 0.5145 (pm20) outliers start: 15 outliers final: 12 residues processed: 60 average time/residue: 0.1198 time to fit residues: 8.5794 Evaluate side-chains 63 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 87 VAL Chi-restraints excluded: chain R residue 116 MET Chi-restraints excluded: chain R residue 124 ILE 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 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: 0.5980 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.167948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.133819 restraints weight = 2774.734| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.71 r_work: 0.3546 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2151 Z= 0.181 Angle : 0.609 7.790 2926 Z= 0.295 Chirality : 0.039 0.153 364 Planarity : 0.003 0.024 344 Dihedral : 4.196 23.570 285 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 6.38 % Allowed : 31.06 % 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: 2.27 (0.56), residues: 255 helix: 1.86 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -0.36 (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 0.013 0.001 PHE R 197 TYR 0.011 0.001 TYR R 277 ARG 0.008 0.001 ARG R 302 *********************** 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 64 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.242 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 59 average time/residue: 0.1376 time to fit residues: 9.8454 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 : 0.231 ------------------------------------------------------------------------------- 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 116 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 175 CYS 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 206 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.0470 chunk 13 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.168981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.134940 restraints weight = 2739.954| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.69 r_work: 0.3567 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2151 Z= 0.165 Angle : 0.598 7.801 2926 Z= 0.289 Chirality : 0.039 0.153 364 Planarity : 0.003 0.025 344 Dihedral : 4.140 23.186 285 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.81 % Allowed : 30.64 % 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: 2.33 (0.56), residues: 255 helix: 1.89 (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 0.001 0.000 HIS R 261 PHE 0.020 0.001 PHE R 197 TYR 0.011 0.001 TYR R 277 ARG 0.008 0.001 ARG R 302 ********************** 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 67 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.220 Fit side-chains outliers start: 16 outliers final: 15 residues processed: 60 average time/residue: 0.1117 time to fit residues: 8.0718 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 : 0.218 ------------------------------------------------------------------------------- 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 87 VAL Chi-restraints excluded: chain R residue 116 MET Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 175 CYS 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 206 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.0040 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.168602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134497 restraints weight = 2723.362| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.68 r_work: 0.3548 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2151 Z= 0.173 Angle : 0.598 7.679 2926 Z= 0.290 Chirality : 0.039 0.153 364 Planarity : 0.003 0.027 344 Dihedral : 4.137 23.115 285 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 6.81 % Allowed : 30.64 % 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: 2.34 (0.56), residues: 255 helix: 1.90 (0.37), 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 0.001 0.000 HIS R 261 PHE 0.010 0.001 PHE R 197 TYR 0.011 0.001 TYR R 277 ARG 0.007 0.001 ARG R 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1511.10 seconds wall clock time: 26 minutes 58.03 seconds (1618.03 seconds total)