Starting phenix.real_space_refine on Sat Apr 26 15:37:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfb_60055/04_2025/8zfb_60055.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfb_60055/04_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_60055/04_2025/8zfb_60055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfb_60055/04_2025/8zfb_60055.map" model { file = "/net/cci-nas-00/data/ceres_data/8zfb_60055/04_2025/8zfb_60055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfb_60055/04_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-5669/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: 2.54, per 1000 atoms: 1.22 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 259.8 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: 0.19 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: 0.49 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.460 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.200 ------------------------------------------------------------------------------- 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 : 0.228 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.2840 time to fit residues: 6.1204 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 : 0.223 ------------------------------------------------------------------------------- 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: 0.3980 chunk 25 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.0770 overall best weight: 0.1736 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.149117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144206 restraints weight = 2903.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.144677 restraints weight = 2395.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.144677 restraints weight = 2005.352| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2144 Z= 0.166 Angle : 0.703 5.920 2937 Z= 0.349 Chirality : 0.043 0.186 338 Planarity : 0.007 0.046 373 Dihedral : 5.519 50.941 317 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.59 % Allowed : 7.25 % Favored : 90.16 % 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: 0.64 (0.53), residues: 282 helix: 1.40 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -2.96 (0.75), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 83 HIS 0.004 0.001 HIS R 276 PHE 0.013 0.002 PHE R 107 TYR 0.015 0.002 TYR R 76 ARG 0.001 0.000 ARG R 129 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 157) hydrogen bonds : angle 4.66059 ( 471) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.71477 ( 2) covalent geometry : bond 0.00365 ( 2143) covalent geometry : angle 0.70326 ( 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 : 0.222 Fit side-chains REVERT: R 206 LEU cc_start: 0.7603 (mm) cc_final: 0.7010 (mp) outliers start: 5 outliers final: 4 residues processed: 19 average time/residue: 0.2739 time to fit residues: 5.9296 Evaluate side-chains 20 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 81 ASP 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: 0.9990 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 20 optimal weight: 0.0870 chunk 4 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 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 = 0.3813 r_free = 0.3813 target = 0.148033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142479 restraints weight = 2932.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.142821 restraints weight = 2460.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.142830 restraints weight = 2175.936| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2144 Z= 0.177 Angle : 0.675 5.979 2937 Z= 0.340 Chirality : 0.043 0.134 338 Planarity : 0.007 0.047 373 Dihedral : 5.632 57.097 317 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.07 % Allowed : 12.44 % Favored : 85.49 % 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: 1.63 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -3.00 (0.77), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP R 83 HIS 0.004 0.001 HIS R 276 PHE 0.014 0.002 PHE R 107 TYR 0.013 0.001 TYR R 76 ARG 0.002 0.000 ARG R 129 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 157) hydrogen bonds : angle 4.56699 ( 471) SS BOND : bond 0.00001 ( 1) SS BOND : angle 0.97361 ( 2) covalent geometry : bond 0.00392 ( 2143) covalent geometry : angle 0.67452 ( 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 24 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.457 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 22 average time/residue: 0.2418 time to fit residues: 6.1233 Evaluate side-chains 20 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 ASP 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: 0.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 overall best weight: 0.2378 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.147948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143002 restraints weight = 2884.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.143154 restraints weight = 2561.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.143216 restraints weight = 2214.828| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2144 Z= 0.185 Angle : 0.670 6.089 2937 Z= 0.339 Chirality : 0.043 0.128 338 Planarity : 0.007 0.046 373 Dihedral : 5.598 54.461 317 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.59 % Allowed : 12.44 % 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: 0.94 (0.54), residues: 282 helix: 1.66 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -3.05 (0.78), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 43 HIS 0.003 0.001 HIS R 242 PHE 0.014 0.002 PHE R 107 TYR 0.014 0.001 TYR R 76 ARG 0.002 0.000 ARG R 129 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 157) hydrogen bonds : angle 4.53304 ( 471) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.30027 ( 2) covalent geometry : bond 0.00418 ( 2143) covalent geometry : angle 0.67028 ( 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 22 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.200 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 19 average time/residue: 0.2629 time to fit residues: 5.7026 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 : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 ASP Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 198 MET Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 206 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 2 optimal weight: 0.2980 chunk 11 optimal weight: 0.0060 chunk 7 optimal weight: 0.0070 chunk 3 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 overall best weight: 0.0792 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.150410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144985 restraints weight = 2927.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.145539 restraints weight = 2430.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145625 restraints weight = 2076.030| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.1628 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= 0.129 Angle : 0.622 7.357 2937 Z= 0.307 Chirality : 0.041 0.249 338 Planarity : 0.006 0.048 373 Dihedral : 5.228 52.133 317 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % 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: 1.46 (0.55), residues: 282 helix: 2.01 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -2.87 (0.81), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 43 HIS 0.002 0.001 HIS R 242 PHE 0.011 0.001 PHE R 107 TYR 0.010 0.001 TYR R 76 ARG 0.002 0.000 ARG R 210 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 157) hydrogen bonds : angle 4.25216 ( 471) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.17688 ( 2) covalent geometry : bond 0.00273 ( 2143) covalent geometry : angle 0.62213 ( 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 19 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.374 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 17 average time/residue: 0.2845 time to fit residues: 5.5094 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 : 0.219 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.0970 chunk 23 optimal weight: 0.2980 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 0.0370 chunk 17 optimal weight: 0.1980 chunk 26 optimal weight: 0.0980 chunk 25 optimal weight: 0.0770 chunk 10 optimal weight: 0.0670 chunk 2 optimal weight: 0.0970 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 overall best weight: 0.0750 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.151943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146562 restraints weight = 2902.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146562 restraints weight = 2318.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146562 restraints weight = 2318.985| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.1905 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 : 0.590 6.222 2937 Z= 0.293 Chirality : 0.040 0.194 338 Planarity : 0.006 0.048 373 Dihedral : 3.670 11.563 315 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.55 % Allowed : 17.10 % Favored : 81.35 % 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: 1.84 (0.56), residues: 282 helix: 2.36 (0.38), residues: 216 sheet: None (None), residues: 0 loop : -2.93 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 43 HIS 0.002 0.001 HIS R 242 PHE 0.010 0.001 PHE R 107 TYR 0.012 0.001 TYR R 76 ARG 0.001 0.000 ARG R 270 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 157) hydrogen bonds : angle 4.03424 ( 471) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.21470 ( 2) covalent geometry : bond 0.00261 ( 2143) covalent geometry : angle 0.59067 ( 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 17 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 14 time to evaluate : 0.218 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 15 average time/residue: 0.3006 time to fit residues: 5.2823 Evaluate side-chains 16 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0870 chunk 24 optimal weight: 0.0970 chunk 21 optimal weight: 0.4980 chunk 4 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 0.0030 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 5 optimal weight: 0.0870 chunk 16 optimal weight: 0.0970 overall best weight: 0.0722 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.152513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.147267 restraints weight = 2962.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.147365 restraints weight = 2315.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.147682 restraints weight = 2185.424| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2144 Z= 0.121 Angle : 0.611 9.425 2937 Z= 0.296 Chirality : 0.041 0.261 338 Planarity : 0.006 0.049 373 Dihedral : 3.591 11.579 315 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: 1.99 (0.55), residues: 282 helix: 2.45 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -2.92 (0.79), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 43 HIS 0.002 0.001 HIS R 242 PHE 0.010 0.001 PHE R 107 TYR 0.010 0.001 TYR R 76 ARG 0.001 0.000 ARG R 270 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 157) hydrogen bonds : angle 3.97073 ( 471) SS BOND : bond 0.00052 ( 1) SS BOND : angle 0.13584 ( 2) covalent geometry : bond 0.00257 ( 2143) covalent geometry : angle 0.61115 ( 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 23 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.218 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 21 average time/residue: 0.2734 time to fit residues: 6.5541 Evaluate side-chains 22 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 188 LEU 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: 0.6980 chunk 11 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 17 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 8 optimal weight: 0.3980 chunk 1 optimal weight: 0.0060 chunk 23 optimal weight: 0.0980 chunk 26 optimal weight: 0.1980 overall best weight: 0.1154 ------------------------------------------------------------------------------- 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 = 0.151773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146350 restraints weight = 2997.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.146778 restraints weight = 2427.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.146778 restraints weight = 2145.583| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.2057 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= 0.133 Angle : 0.627 9.651 2937 Z= 0.302 Chirality : 0.042 0.286 338 Planarity : 0.006 0.048 373 Dihedral : 3.623 11.686 315 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.11 % Allowed : 16.58 % Favored : 80.31 % 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: 1.94 (0.55), residues: 282 helix: 2.41 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -2.88 (0.79), 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 242 PHE 0.012 0.001 PHE R 107 TYR 0.011 0.001 TYR R 76 ARG 0.001 0.000 ARG R 129 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 157) hydrogen bonds : angle 3.99483 ( 471) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.20188 ( 2) covalent geometry : bond 0.00294 ( 2143) covalent geometry : angle 0.62748 ( 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 22 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.223 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 19 average time/residue: 0.2559 time to fit residues: 5.5956 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 : 0.167 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.0670 chunk 5 optimal weight: 0.0980 chunk 19 optimal weight: 0.0270 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.0010 chunk 9 optimal weight: 0.0970 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 overall best weight: 0.0578 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.154175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.149553 restraints weight = 3007.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.149931 restraints weight = 2333.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.149931 restraints weight = 2010.289| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.2364 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= 0.117 Angle : 0.608 9.724 2937 Z= 0.290 Chirality : 0.041 0.297 338 Planarity : 0.006 0.049 373 Dihedral : 3.443 11.552 315 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.11 % Allowed : 16.58 % Favored : 80.31 % 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: 2.13 (0.55), residues: 282 helix: 2.43 (0.37), residues: 222 sheet: None (None), residues: 0 loop : -2.78 (0.79), 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 115 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 157) hydrogen bonds : angle 3.83637 ( 471) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.10127 ( 2) covalent geometry : bond 0.00251 ( 2143) covalent geometry : angle 0.60802 ( 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 26 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.223 Fit side-chains REVERT: R 236 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7095 (tt) outliers start: 6 outliers final: 5 residues processed: 23 average time/residue: 0.2418 time to fit residues: 6.3804 Evaluate side-chains 25 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 11 optimal weight: 0.3980 chunk 5 optimal weight: 0.0970 chunk 25 optimal weight: 0.0170 chunk 3 optimal weight: 0.2980 chunk 14 optimal weight: 0.0060 chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 0.3980 chunk 6 optimal weight: 0.0670 chunk 4 optimal weight: 0.0020 overall best weight: 0.0378 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.155536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.149899 restraints weight = 2930.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.150424 restraints weight = 2381.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.150424 restraints weight = 2061.709| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2144 Z= 0.116 Angle : 0.633 9.772 2937 Z= 0.303 Chirality : 0.041 0.294 338 Planarity : 0.006 0.050 373 Dihedral : 3.541 16.253 315 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.63 % Allowed : 16.06 % Favored : 80.31 % 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: 2.26 (0.55), residues: 282 helix: 2.53 (0.37), residues: 222 sheet: None (None), residues: 0 loop : -2.80 (0.77), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 43 HIS 0.003 0.001 HIS R 165 PHE 0.009 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 0.02909 ( 157) hydrogen bonds : angle 3.79482 ( 471) SS BOND : bond 0.00789 ( 1) SS BOND : angle 2.62680 ( 2) covalent geometry : bond 0.00249 ( 2143) covalent geometry : angle 0.62956 ( 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 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.227 Fit side-chains REVERT: R 236 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7068 (tt) outliers start: 7 outliers final: 3 residues processed: 26 average time/residue: 0.2380 time to fit residues: 7.0443 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 206 LEU Chi-restraints excluded: chain R residue 207 ARG Chi-restraints excluded: chain R residue 236 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 0.0000 chunk 17 optimal weight: 0.0050 chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 0.0970 chunk 10 optimal weight: 0.0870 chunk 19 optimal weight: 0.2980 chunk 26 optimal weight: 0.0980 chunk 11 optimal weight: 0.0870 chunk 25 optimal weight: 0.0770 chunk 3 optimal weight: 0.0870 chunk 22 optimal weight: 0.3980 overall best weight: 0.0512 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.155782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.150007 restraints weight = 2957.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.150555 restraints weight = 2414.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.150673 restraints weight = 2106.401| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.2695 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= 0.120 Angle : 0.655 9.698 2937 Z= 0.316 Chirality : 0.042 0.295 338 Planarity : 0.006 0.050 373 Dihedral : 3.615 16.176 315 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.59 % Allowed : 17.10 % Favored : 80.31 % 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: 2.27 (0.55), residues: 282 helix: 2.56 (0.37), residues: 223 sheet: None (None), residues: 0 loop : -2.96 (0.78), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 43 HIS 0.001 0.000 HIS R 242 PHE 0.009 0.001 PHE R 107 TYR 0.006 0.001 TYR R 55 ARG 0.001 0.000 ARG R 270 Details of bonding type rmsd hydrogen bonds : bond 0.02963 ( 157) hydrogen bonds : angle 3.78389 ( 471) SS BOND : bond 0.00418 ( 1) SS BOND : angle 1.98305 ( 2) covalent geometry : bond 0.00260 ( 2143) covalent geometry : angle 0.65339 ( 2935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1318.88 seconds wall clock time: 23 minutes 29.22 seconds (1409.22 seconds total)