Starting phenix.real_space_refine on Fri May 9 13:21:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfb_60055/05_2025/8zfb_60055.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfb_60055/05_2025/8zfb_60055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zfb_60055/05_2025/8zfb_60055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfb_60055/05_2025/8zfb_60055.map" model { file = "/net/cci-nas-00/data/ceres_data/8zfb_60055/05_2025/8zfb_60055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfb_60055/05_2025/8zfb_60055.cif" } resolution = 3.78 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 1359 2.51 5 N 363 2.21 5 O 352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2088 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2088 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 267} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 2.73, per 1000 atoms: 1.31 Number of scatterers: 2088 At special positions: 0 Unit cell: (59.36, 71.02, 72.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 352 8.00 N 363 7.00 C 1359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " 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=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 288.6 milliseconds 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 526 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 18 through 47 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 50 through 79 removed outlier: 4.143A pdb=" N VAL R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 89 through 121 removed outlier: 4.137A pdb=" N PHE R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 150 removed outlier: 4.035A pdb=" N SER R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 191 removed outlier: 4.224A pdb=" N VAL R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 209 Processing helix chain 'R' and resid 210 through 212 No H-bonds generated for 'chain 'R' and resid 210 through 212' Processing helix chain 'R' and resid 216 through 228 removed outlier: 3.866A pdb=" N ARG R 222 " --> pdb=" O ARG R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 239 Processing helix chain 'R' and resid 239 through 254 Processing helix chain 'R' and resid 264 through 283 Proline residue: R 273 - end of helix removed outlier: 3.795A pdb=" N ALA R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU R 279 " --> pdb=" O TYR R 275 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA R 280 " --> pdb=" O HIS R 276 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU R 281 " --> pdb=" O ALA R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 294 Proline residue: R 290 - end of helix Processing helix chain 'R' and resid 297 through 308 157 hydrogen bonds defined for protein. 471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.54 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 320 1.31 - 1.43: 597 1.43 - 1.56: 1210 1.56 - 1.68: 0 1.68 - 1.81: 16 Bond restraints: 2143 Sorted by residual: bond pdb=" C SER R 171 " pdb=" O SER R 171 " ideal model delta sigma weight residual 1.233 1.184 0.049 1.35e-02 5.49e+03 1.30e+01 bond pdb=" C THR R 166 " pdb=" O THR R 166 " ideal model delta sigma weight residual 1.232 1.194 0.038 1.44e-02 4.82e+03 7.12e+00 bond pdb=" CA THR R 166 " pdb=" C THR R 166 " ideal model delta sigma weight residual 1.531 1.502 0.030 1.46e-02 4.69e+03 4.12e+00 bond pdb=" CA ARG R 79 " pdb=" C ARG R 79 " ideal model delta sigma weight residual 1.524 1.554 -0.029 1.48e-02 4.57e+03 3.92e+00 bond pdb=" CA SER R 171 " pdb=" C SER R 171 " ideal model delta sigma weight residual 1.526 1.497 0.028 1.51e-02 4.39e+03 3.54e+00 ... (remaining 2138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 2888 3.17 - 6.34: 37 6.34 - 9.51: 7 9.51 - 12.68: 1 12.68 - 15.84: 2 Bond angle restraints: 2935 Sorted by residual: angle pdb=" C TYR R 169 " pdb=" CA TYR R 169 " pdb=" CB TYR R 169 " ideal model delta sigma weight residual 111.48 95.64 15.84 1.59e+00 3.96e-01 9.93e+01 angle pdb=" N GLU R 170 " pdb=" CA GLU R 170 " pdb=" C GLU R 170 " ideal model delta sigma weight residual 110.55 123.97 -13.42 1.35e+00 5.49e-01 9.88e+01 angle pdb=" N TYR R 85 " pdb=" CA TYR R 85 " pdb=" C TYR R 85 " ideal model delta sigma weight residual 111.14 118.40 -7.26 1.08e+00 8.57e-01 4.52e+01 angle pdb=" N SER R 171 " pdb=" CA SER R 171 " pdb=" C SER R 171 " ideal model delta sigma weight residual 107.71 119.35 -11.64 1.90e+00 2.77e-01 3.75e+01 angle pdb=" N ARG R 79 " pdb=" CA ARG R 79 " pdb=" C ARG R 79 " ideal model delta sigma weight residual 112.72 106.12 6.60 1.14e+00 7.69e-01 3.35e+01 ... (remaining 2930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.10: 1061 12.10 - 24.20: 121 24.20 - 36.30: 52 36.30 - 48.40: 10 48.40 - 60.50: 5 Dihedral angle restraints: 1249 sinusoidal: 425 harmonic: 824 Sorted by residual: dihedral pdb=" C ASP R 81 " pdb=" N ASP R 81 " pdb=" CA ASP R 81 " pdb=" CB ASP R 81 " ideal model delta harmonic sigma weight residual -122.60 -136.86 14.26 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" N ASP R 81 " pdb=" C ASP R 81 " pdb=" CA ASP R 81 " pdb=" CB ASP R 81 " ideal model delta harmonic sigma weight residual 122.80 137.04 -14.24 0 2.50e+00 1.60e-01 3.24e+01 dihedral pdb=" C TYR R 169 " pdb=" N TYR R 169 " pdb=" CA TYR R 169 " pdb=" CB TYR R 169 " ideal model delta harmonic sigma weight residual -122.60 -109.80 -12.80 0 2.50e+00 1.60e-01 2.62e+01 ... (remaining 1246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 321 0.115 - 0.229: 10 0.229 - 0.343: 5 0.343 - 0.458: 0 0.458 - 0.572: 2 Chirality restraints: 338 Sorted by residual: chirality pdb=" CA ASP R 81 " pdb=" N ASP R 81 " pdb=" C ASP R 81 " pdb=" CB ASP R 81 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.17e+00 chirality pdb=" CA GLU R 170 " pdb=" N GLU R 170 " pdb=" C GLU R 170 " pdb=" CB GLU R 170 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.86e+00 chirality pdb=" CA CYS R 90 " pdb=" N CYS R 90 " pdb=" C CYS R 90 " pdb=" CB CYS R 90 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 335 not shown) Planarity restraints: 373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 129 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO R 130 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO R 130 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 130 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 71 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO R 72 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO R 72 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 72 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 239 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO R 240 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO R 240 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 240 " -0.026 5.00e-02 4.00e+02 ... (remaining 370 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 9 2.41 - 3.03: 1227 3.03 - 3.65: 3283 3.65 - 4.28: 4382 4.28 - 4.90: 7230 Nonbonded interactions: 16131 Sorted by model distance: nonbonded pdb=" O TYR R 169 " pdb=" CG TYR R 169 " model vdw 1.786 3.260 nonbonded pdb=" O TYR R 169 " pdb=" CD1 TYR R 169 " model vdw 1.841 3.340 nonbonded pdb=" O ASP R 81 " pdb=" OD1 ASP R 81 " model vdw 1.994 3.040 nonbonded pdb=" C ASP R 81 " pdb=" OD1 ASP R 81 " model vdw 2.208 3.270 nonbonded pdb=" OD1 ASN R 58 " pdb=" OG SER R 138 " model vdw 2.276 3.040 ... (remaining 16126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.600 Set stop_for_unknowns flag: 0.010 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: 0.020 Set scattering table: 0.030 Process input model: 11.620 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5284 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 : 0.005 0.055 2144 Z= 0.255 Angle : 0.978 15.844 2937 Z= 0.608 Chirality : 0.074 0.572 338 Planarity : 0.007 0.049 373 Dihedral : 13.254 60.500 720 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.52 % Allowed : 2.59 % Favored : 96.89 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 11.11 % 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: 0.06 (0.53), residues: 282 helix: 0.83 (0.37), residues: 214 sheet: None (None), residues: 0 loop : -2.47 (0.78), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 83 HIS 0.006 0.001 HIS R 276 PHE 0.011 0.002 PHE R 107 TYR 0.014 0.002 TYR R 169 ARG 0.003 0.000 ARG R 80 Details of bonding type rmsd hydrogen bonds : bond 0.11754 ( 157) hydrogen bonds : angle 5.67298 ( 471) SS BOND : bond 0.00444 ( 1) SS BOND : angle 1.16551 ( 2) covalent geometry : bond 0.00478 ( 2143) covalent geometry : angle 0.97814 ( 2935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.214 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.2742 time to fit residues: 5.9053 Evaluate side-chains 19 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 7 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.0060 chunk 25 optimal weight: 0.0970 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 0.0770 overall best weight: 0.0952 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.151121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.145905 restraints weight = 2955.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145820 restraints weight = 2833.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.146192 restraints weight = 2499.609| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2144 Z= 0.143 Angle : 0.671 6.468 2937 Z= 0.332 Chirality : 0.041 0.198 338 Planarity : 0.007 0.048 373 Dihedral : 5.523 51.464 317 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.59 % Allowed : 6.74 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.92 (0.54), residues: 282 helix: 1.62 (0.37), residues: 215 sheet: None (None), residues: 0 loop : -2.88 (0.76), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 83 HIS 0.003 0.001 HIS R 276 PHE 0.011 0.001 PHE R 107 TYR 0.013 0.001 TYR R 76 ARG 0.002 0.000 ARG R 210 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 157) hydrogen bonds : angle 4.51083 ( 471) SS BOND : bond 0.00147 ( 1) SS BOND : angle 0.72022 ( 2) covalent geometry : bond 0.00299 ( 2143) covalent geometry : angle 0.67062 ( 2935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.203 Fit side-chains REVERT: R 206 LEU cc_start: 0.7617 (mm) cc_final: 0.7015 (mp) outliers start: 5 outliers final: 3 residues processed: 19 average time/residue: 0.2624 time to fit residues: 5.6770 Evaluate side-chains 18 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 199 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.0670 chunk 23 optimal weight: 0.0980 chunk 14 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 9 optimal weight: 0.1980 chunk 20 optimal weight: 0.0670 chunk 4 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 overall best weight: 0.0856 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.152619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.146927 restraints weight = 2943.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147162 restraints weight = 2333.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.147519 restraints weight = 2084.359| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5915 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2144 Z= 0.127 Angle : 0.601 6.118 2937 Z= 0.302 Chirality : 0.039 0.132 338 Planarity : 0.006 0.049 373 Dihedral : 3.760 11.599 315 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.55 % Allowed : 10.36 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.59 (0.56), residues: 282 helix: 2.13 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -2.83 (0.80), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 43 HIS 0.004 0.001 HIS R 276 PHE 0.011 0.001 PHE R 107 TYR 0.014 0.001 TYR R 76 ARG 0.001 0.000 ARG R 129 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 157) hydrogen bonds : angle 4.15805 ( 471) SS BOND : bond 0.00065 ( 1) SS BOND : angle 0.89765 ( 2) covalent geometry : bond 0.00270 ( 2143) covalent geometry : angle 0.60043 ( 2935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.202 Fit side-chains REVERT: R 206 LEU cc_start: 0.7627 (mm) cc_final: 0.7031 (mp) REVERT: R 225 ARG cc_start: 0.6094 (mmt180) cc_final: 0.5856 (mmt180) outliers start: 3 outliers final: 1 residues processed: 18 average time/residue: 0.3075 time to fit residues: 6.2088 Evaluate side-chains 18 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 188 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 0 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 11 optimal weight: 0.0980 chunk 17 optimal weight: 0.4980 chunk 12 optimal weight: 0.0970 chunk 18 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 overall best weight: 0.2156 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.148281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.142716 restraints weight = 2894.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143257 restraints weight = 2403.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143666 restraints weight = 2051.868| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2144 Z= 0.174 Angle : 0.666 6.132 2937 Z= 0.332 Chirality : 0.043 0.176 338 Planarity : 0.007 0.047 373 Dihedral : 4.066 12.528 315 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.07 % Allowed : 12.95 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.32 (0.55), residues: 282 helix: 1.96 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -3.02 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 83 HIS 0.004 0.001 HIS R 276 PHE 0.015 0.002 PHE R 107 TYR 0.014 0.001 TYR R 76 ARG 0.002 0.000 ARG R 79 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 157) hydrogen bonds : angle 4.36775 ( 471) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.70506 ( 2) covalent geometry : bond 0.00390 ( 2143) covalent geometry : angle 0.66559 ( 2935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.201 Fit side-chains REVERT: R 225 ARG cc_start: 0.6173 (mmt180) cc_final: 0.5743 (mpt180) outliers start: 4 outliers final: 2 residues processed: 18 average time/residue: 0.2681 time to fit residues: 5.4856 Evaluate side-chains 17 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 199 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 0.0870 chunk 25 optimal weight: 0.0870 chunk 2 optimal weight: 0.0970 chunk 11 optimal weight: 0.0270 chunk 7 optimal weight: 0.0470 chunk 3 optimal weight: 0.1980 chunk 6 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 13 optimal weight: 0.4980 overall best weight: 0.0690 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.151818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.146434 restraints weight = 2923.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.146867 restraints weight = 2464.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.147345 restraints weight = 2124.783| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2144 Z= 0.123 Angle : 0.585 6.191 2937 Z= 0.291 Chirality : 0.038 0.123 338 Planarity : 0.006 0.049 373 Dihedral : 3.685 11.610 315 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.07 % Allowed : 12.95 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.85 (0.56), residues: 282 helix: 2.33 (0.38), residues: 217 sheet: None (None), residues: 0 loop : -2.86 (0.80), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 43 HIS 0.002 0.001 HIS R 242 PHE 0.009 0.001 PHE R 107 TYR 0.010 0.001 TYR R 76 ARG 0.001 0.000 ARG R 79 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 157) hydrogen bonds : angle 4.03310 ( 471) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.29392 ( 2) covalent geometry : bond 0.00261 ( 2143) covalent geometry : angle 0.58562 ( 2935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.235 Fit side-chains REVERT: R 225 ARG cc_start: 0.6059 (mmt180) cc_final: 0.5853 (mpt180) outliers start: 4 outliers final: 3 residues processed: 16 average time/residue: 0.2956 time to fit residues: 5.3691 Evaluate side-chains 17 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 206 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.0870 chunk 23 optimal weight: 0.0870 chunk 18 optimal weight: 0.1980 chunk 27 optimal weight: 0.1980 chunk 17 optimal weight: 0.1980 chunk 26 optimal weight: 0.1980 chunk 25 optimal weight: 0.0670 chunk 10 optimal weight: 0.0970 chunk 2 optimal weight: 0.0870 chunk 4 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 overall best weight: 0.0810 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.151858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146422 restraints weight = 2916.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.147019 restraints weight = 2371.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.147019 restraints weight = 2014.454| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2144 Z= 0.124 Angle : 0.604 7.314 2937 Z= 0.293 Chirality : 0.040 0.242 338 Planarity : 0.006 0.048 373 Dihedral : 3.580 11.576 315 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.55 % Allowed : 15.54 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.96 (0.55), residues: 282 helix: 2.43 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -2.95 (0.78), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 43 HIS 0.002 0.001 HIS R 276 PHE 0.011 0.001 PHE R 107 TYR 0.010 0.001 TYR R 76 ARG 0.001 0.000 ARG R 129 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 157) hydrogen bonds : angle 3.98624 ( 471) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.26181 ( 2) covalent geometry : bond 0.00267 ( 2143) covalent geometry : angle 0.60374 ( 2935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.213 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 20 average time/residue: 0.2410 time to fit residues: 5.5385 Evaluate side-chains 21 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 206 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.0170 chunk 24 optimal weight: 0.2980 chunk 21 optimal weight: 0.0370 chunk 4 optimal weight: 0.2980 chunk 22 optimal weight: 0.2980 chunk 3 optimal weight: 0.0010 chunk 8 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 5 optimal weight: 0.0870 chunk 16 optimal weight: 0.4980 overall best weight: 0.0880 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.152333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146867 restraints weight = 2978.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.147370 restraints weight = 2490.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.147764 restraints weight = 2110.462| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2144 Z= 0.123 Angle : 0.598 6.776 2937 Z= 0.290 Chirality : 0.040 0.227 338 Planarity : 0.006 0.049 373 Dihedral : 3.533 11.805 315 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.07 % Allowed : 15.54 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.55), residues: 282 helix: 2.35 (0.37), residues: 221 sheet: None (None), residues: 0 loop : -2.75 (0.79), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 43 HIS 0.002 0.001 HIS R 242 PHE 0.011 0.001 PHE R 107 TYR 0.009 0.001 TYR R 76 ARG 0.001 0.000 ARG R 224 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 157) hydrogen bonds : angle 3.92391 ( 471) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.26751 ( 2) covalent geometry : bond 0.00270 ( 2143) covalent geometry : angle 0.59780 ( 2935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.222 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 20 average time/residue: 0.2464 time to fit residues: 5.6241 Evaluate side-chains 20 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 206 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 12 optimal weight: 0.3980 chunk 11 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.0470 chunk 17 optimal weight: 0.0970 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 8 optimal weight: 0.4980 chunk 1 optimal weight: 0.0980 chunk 23 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 overall best weight: 0.1276 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.151769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.146862 restraints weight = 3003.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.147138 restraints weight = 2777.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.147443 restraints weight = 2458.163| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2144 Z= 0.136 Angle : 0.628 9.766 2937 Z= 0.301 Chirality : 0.042 0.294 338 Planarity : 0.006 0.048 373 Dihedral : 3.600 11.759 315 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.07 % Allowed : 16.06 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.97 (0.55), residues: 282 helix: 2.31 (0.37), residues: 221 sheet: None (None), residues: 0 loop : -2.75 (0.80), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 43 HIS 0.002 0.001 HIS R 242 PHE 0.012 0.001 PHE R 107 TYR 0.010 0.001 TYR R 76 ARG 0.001 0.000 ARG R 129 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 157) hydrogen bonds : angle 4.01315 ( 471) SS BOND : bond 0.00097 ( 1) SS BOND : angle 0.27263 ( 2) covalent geometry : bond 0.00304 ( 2143) covalent geometry : angle 0.62798 ( 2935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.215 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 20 average time/residue: 0.2451 time to fit residues: 5.6249 Evaluate side-chains 21 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 206 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 13 optimal weight: 0.0570 chunk 7 optimal weight: 0.0070 chunk 24 optimal weight: 0.0070 chunk 9 optimal weight: 0.2980 chunk 17 optimal weight: 0.1980 chunk 2 optimal weight: 0.0970 overall best weight: 0.0532 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.154778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.149769 restraints weight = 3000.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.150197 restraints weight = 2392.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.150781 restraints weight = 2052.750| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2144 Z= 0.116 Angle : 0.608 10.610 2937 Z= 0.287 Chirality : 0.041 0.319 338 Planarity : 0.006 0.049 373 Dihedral : 3.399 11.490 315 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.07 % Allowed : 16.06 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.24 (0.55), residues: 282 helix: 2.52 (0.37), residues: 222 sheet: None (None), residues: 0 loop : -2.82 (0.79), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 43 HIS 0.002 0.001 HIS R 242 PHE 0.009 0.001 PHE R 107 TYR 0.008 0.001 TYR R 76 ARG 0.001 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 157) hydrogen bonds : angle 3.84429 ( 471) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.03577 ( 2) covalent geometry : bond 0.00248 ( 2143) covalent geometry : angle 0.60805 ( 2935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.226 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 24 average time/residue: 0.2410 time to fit residues: 6.5832 Evaluate side-chains 25 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 207 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 0.0670 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 0.0770 chunk 22 optimal weight: 0.0870 chunk 17 optimal weight: 0.0980 chunk 6 optimal weight: 0.4980 chunk 4 optimal weight: 0.3980 overall best weight: 0.0832 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.153625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.148928 restraints weight = 2943.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.149277 restraints weight = 2330.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.149277 restraints weight = 2028.075| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2144 Z= 0.121 Angle : 0.615 10.638 2937 Z= 0.290 Chirality : 0.042 0.311 338 Planarity : 0.006 0.048 373 Dihedral : 3.390 11.352 315 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.59 % Allowed : 15.54 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.21 (0.55), residues: 282 helix: 2.50 (0.37), residues: 222 sheet: None (None), residues: 0 loop : -2.82 (0.79), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 43 HIS 0.002 0.001 HIS R 242 PHE 0.010 0.001 PHE R 107 TYR 0.009 0.001 TYR R 76 ARG 0.001 0.000 ARG R 270 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 157) hydrogen bonds : angle 3.86318 ( 471) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.16679 ( 2) covalent geometry : bond 0.00267 ( 2143) covalent geometry : angle 0.61473 ( 2935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.198 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 20 average time/residue: 0.2721 time to fit residues: 6.1193 Evaluate side-chains 22 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 207 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 0.0060 chunk 17 optimal weight: 0.0010 chunk 9 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 19 optimal weight: 0.2980 chunk 26 optimal weight: 0.4980 chunk 11 optimal weight: 0.0270 chunk 25 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 overall best weight: 0.0438 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.156156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.151082 restraints weight = 2949.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151533 restraints weight = 2351.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.151591 restraints weight = 2065.776| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2144 Z= 0.112 Angle : 0.599 10.512 2937 Z= 0.281 Chirality : 0.041 0.314 338 Planarity : 0.006 0.049 373 Dihedral : 3.242 11.284 315 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.11 % Allowed : 15.03 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.37 (0.55), residues: 282 helix: 2.65 (0.37), residues: 222 sheet: None (None), residues: 0 loop : -2.93 (0.77), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 43 HIS 0.002 0.000 HIS R 242 PHE 0.009 0.001 PHE R 107 TYR 0.008 0.001 TYR R 76 ARG 0.001 0.000 ARG R 270 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 157) hydrogen bonds : angle 3.75188 ( 471) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.10492 ( 2) covalent geometry : bond 0.00241 ( 2143) covalent geometry : angle 0.59966 ( 2935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1235.82 seconds wall clock time: 22 minutes 19.58 seconds (1339.58 seconds total)