Starting phenix.real_space_refine on Wed Mar 5 15:22:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vv4_32137/03_2025/7vv4_32137.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv4_32137/03_2025/7vv4_32137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vv4_32137/03_2025/7vv4_32137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv4_32137/03_2025/7vv4_32137.map" model { file = "/net/cci-nas-00/data/ceres_data/7vv4_32137/03_2025/7vv4_32137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv4_32137/03_2025/7vv4_32137.cif" } resolution = 2.97 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= 0.003 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 18 5.16 5 C 1483 2.51 5 N 338 2.21 5 O 342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2181 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2101 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.05, per 1000 atoms: 0.94 Number of scatterers: 2181 At special positions: 0 Unit cell: (66.276, 73.64, 61.016, 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 18 16.00 O 342 8.00 N 338 7.00 C 1483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.02 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: 0.54 Conformation dependent library (CDL) restraints added in 268.3 milliseconds 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 504 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'R' and resid 27 through 57 removed outlier: 3.691A pdb=" N ILE R 32 " --> pdb=" O LYS R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix removed outlier: 3.657A pdb=" N LEU R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 95 removed outlier: 3.618A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.650A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 168 removed outlier: 3.508A pdb=" N GLU R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS R 168 " --> pdb=" O GLU R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 213 removed outlier: 3.898A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR R 187 " --> pdb=" O PHE R 183 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 235 Processing helix chain 'R' and resid 236 through 244 removed outlier: 4.300A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 251 removed outlier: 3.799A pdb=" N TRP R 248 " --> pdb=" O PHE R 244 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE R 249 " --> pdb=" O LEU R 245 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 259 removed outlier: 4.020A pdb=" N CYS R 258 " --> pdb=" O ASP R 254 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 280 removed outlier: 3.947A pdb=" N VAL R 263 " --> pdb=" O HIS R 259 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 159 hydrogen bonds defined for protein. 477 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: 0.57 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 400 1.33 - 1.45: 605 1.45 - 1.58: 1221 1.58 - 1.70: 1 1.70 - 1.82: 22 Bond restraints: 2249 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.621 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C HIS R 261 " pdb=" O HIS R 261 " ideal model delta sigma weight residual 1.244 1.217 0.027 9.80e-03 1.04e+04 7.64e+00 bond pdb=" C ASN R 271 " pdb=" O ASN R 271 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.89e+00 bond pdb=" N PHE R 76 " pdb=" CA PHE R 76 " ideal model delta sigma weight residual 1.459 1.432 0.027 1.19e-02 7.06e+03 5.26e+00 bond pdb=" C LEU R 267 " pdb=" O LEU R 267 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.15e-02 7.56e+03 5.19e+00 ... (remaining 2244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 2921 2.50 - 5.01: 111 5.01 - 7.51: 27 7.51 - 10.02: 6 10.02 - 12.52: 2 Bond angle restraints: 3067 Sorted by residual: angle pdb=" N LEU R 256 " pdb=" CA LEU R 256 " pdb=" C LEU R 256 " ideal model delta sigma weight residual 111.14 120.33 -9.19 1.08e+00 8.57e-01 7.24e+01 angle pdb=" N SER R 253 " pdb=" CA SER R 253 " pdb=" C SER R 253 " ideal model delta sigma weight residual 111.28 119.10 -7.82 1.09e+00 8.42e-01 5.14e+01 angle pdb=" N ILE R 260 " pdb=" CA ILE R 260 " pdb=" C ILE R 260 " ideal model delta sigma weight residual 110.72 117.16 -6.44 1.01e+00 9.80e-01 4.07e+01 angle pdb=" N ILE R 249 " pdb=" CA ILE R 249 " pdb=" C ILE R 249 " ideal model delta sigma weight residual 110.72 116.86 -6.14 1.01e+00 9.80e-01 3.70e+01 angle pdb=" N ILE R 246 " pdb=" CA ILE R 246 " pdb=" C ILE R 246 " ideal model delta sigma weight residual 110.72 116.82 -6.10 1.01e+00 9.80e-01 3.65e+01 ... (remaining 3062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.12: 1114 14.12 - 28.25: 139 28.25 - 42.37: 53 42.37 - 56.49: 8 56.49 - 70.61: 5 Dihedral angle restraints: 1319 sinusoidal: 542 harmonic: 777 Sorted by residual: dihedral pdb=" C PHE L 25 " pdb=" N PHE L 25 " pdb=" CA PHE L 25 " pdb=" CB PHE L 25 " ideal model delta harmonic sigma weight residual -122.60 -139.87 17.27 0 2.50e+00 1.60e-01 4.77e+01 dihedral pdb=" N PHE L 26 " pdb=" C PHE L 26 " pdb=" CA PHE L 26 " pdb=" CB PHE L 26 " ideal model delta harmonic sigma weight residual 122.80 139.84 -17.04 0 2.50e+00 1.60e-01 4.65e+01 dihedral pdb=" C PHE L 26 " pdb=" N PHE L 26 " pdb=" CA PHE L 26 " pdb=" CB PHE L 26 " ideal model delta harmonic sigma weight residual -122.60 -139.42 16.82 0 2.50e+00 1.60e-01 4.53e+01 ... (remaining 1316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 344 0.157 - 0.313: 13 0.313 - 0.470: 3 0.470 - 0.627: 1 0.627 - 0.783: 1 Chirality restraints: 362 Sorted by residual: chirality pdb=" CA PHE L 26 " pdb=" N PHE L 26 " pdb=" C PHE L 26 " pdb=" CB PHE L 26 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA PHE L 25 " pdb=" N PHE L 25 " pdb=" C PHE L 25 " pdb=" CB PHE L 25 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.18e+00 chirality pdb=" CA HIS R 261 " pdb=" N HIS R 261 " pdb=" C HIS R 261 " pdb=" CB HIS R 261 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.52e+00 ... (remaining 359 not shown) Planarity restraints: 356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 32 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO R 33 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 33 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 33 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 241 " -0.010 2.00e-02 2.50e+03 2.17e-02 4.69e+00 pdb=" C ILE R 241 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 241 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN R 242 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 30 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C THR R 30 " 0.022 2.00e-02 2.50e+03 pdb=" O THR R 30 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU R 31 " -0.007 2.00e-02 2.50e+03 ... (remaining 353 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 4 2.26 - 2.92: 866 2.92 - 3.58: 3261 3.58 - 4.24: 4665 4.24 - 4.90: 8093 Nonbonded interactions: 16889 Sorted by model distance: nonbonded pdb=" OD1 ASP R 75 " pdb=" OG SER R 272 " model vdw 1.600 3.040 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP R 75 " pdb=" CB SER R 272 " model vdw 2.247 3.440 nonbonded pdb=" CB SER R 177 " pdb=" SG CYS L 22 " model vdw 2.259 3.800 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.309 3.040 ... (remaining 16884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.460 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 23.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 2249 Z= 0.418 Angle : 1.197 12.523 3067 Z= 0.708 Chirality : 0.091 0.783 362 Planarity : 0.006 0.069 356 Dihedral : 14.733 70.611 812 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.75 % Allowed : 4.58 % Favored : 91.67 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.49), residues: 265 helix: 0.47 (0.35), residues: 204 sheet: None (None), residues: 0 loop : -3.09 (0.60), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 250 HIS 0.004 0.002 HIS R 261 PHE 0.016 0.002 PHE L 26 TYR 0.011 0.003 TYR R 279 ARG 0.009 0.001 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.221 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 52 average time/residue: 0.5947 time to fit residues: 32.1917 Evaluate side-chains 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 250 TRP Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain L residue 26 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.0040 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.145316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.117562 restraints weight = 3156.833| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.62 r_work: 0.3557 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2249 Z= 0.190 Angle : 0.638 8.043 3067 Z= 0.304 Chirality : 0.041 0.309 362 Planarity : 0.004 0.050 356 Dihedral : 8.998 54.531 357 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.58 % Allowed : 13.75 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.51), residues: 265 helix: 1.81 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -3.42 (0.62), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 248 HIS 0.002 0.001 HIS R 261 PHE 0.018 0.001 PHE R 257 TYR 0.008 0.002 TYR R 279 ARG 0.002 0.000 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.223 Fit side-chains REVERT: R 163 LEU cc_start: 0.7995 (mp) cc_final: 0.7657 (tt) REVERT: R 176 ASP cc_start: 0.7689 (p0) cc_final: 0.7340 (p0) REVERT: R 222 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.6753 (p90) REVERT: R 242 GLN cc_start: 0.8665 (pp30) cc_final: 0.8428 (pp30) REVERT: R 248 TRP cc_start: 0.7571 (m100) cc_final: 0.7243 (m100) outliers start: 11 outliers final: 3 residues processed: 55 average time/residue: 0.6209 time to fit residues: 35.5010 Evaluate side-chains 49 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.0170 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.146850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.118904 restraints weight = 3172.856| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.65 r_work: 0.3581 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2249 Z= 0.155 Angle : 0.610 8.899 3067 Z= 0.279 Chirality : 0.040 0.303 362 Planarity : 0.003 0.042 356 Dihedral : 7.939 49.193 350 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.17 % Allowed : 20.42 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.52), residues: 265 helix: 2.42 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.71 (0.64), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 248 HIS 0.001 0.000 HIS R 261 PHE 0.014 0.001 PHE L 25 TYR 0.009 0.002 TYR R 222 ARG 0.002 0.000 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.215 Fit side-chains REVERT: R 28 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6716 (tmtm) REVERT: R 37 ILE cc_start: 0.7504 (mm) cc_final: 0.7269 (mt) REVERT: R 163 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7475 (tt) REVERT: R 222 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.6827 (p90) REVERT: R 242 GLN cc_start: 0.8668 (pp30) cc_final: 0.8453 (pp30) REVERT: R 248 TRP cc_start: 0.7642 (m100) cc_final: 0.7233 (m100) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 0.5000 time to fit residues: 29.8396 Evaluate side-chains 50 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 LYS Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 246 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.138789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.112074 restraints weight = 3287.243| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.74 r_work: 0.3497 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2249 Z= 0.211 Angle : 0.623 9.470 3067 Z= 0.289 Chirality : 0.043 0.308 362 Planarity : 0.003 0.038 356 Dihedral : 7.853 48.422 350 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.67 % Allowed : 23.33 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.52), residues: 265 helix: 2.47 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.43 (0.66), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 248 HIS 0.003 0.001 HIS R 144 PHE 0.018 0.001 PHE L 25 TYR 0.010 0.002 TYR R 222 ARG 0.005 0.001 ARG R 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.219 Fit side-chains REVERT: R 28 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6755 (tmtm) REVERT: R 86 CYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7164 (p) REVERT: R 216 LEU cc_start: 0.8599 (mp) cc_final: 0.8278 (mp) REVERT: R 222 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6938 (p90) REVERT: R 242 GLN cc_start: 0.8739 (pp30) cc_final: 0.8535 (pp30) outliers start: 16 outliers final: 6 residues processed: 57 average time/residue: 0.5696 time to fit residues: 33.9388 Evaluate side-chains 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 LYS Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.142056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.115279 restraints weight = 3212.124| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.66 r_work: 0.3529 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2249 Z= 0.198 Angle : 0.607 8.251 3067 Z= 0.285 Chirality : 0.043 0.308 362 Planarity : 0.003 0.036 356 Dihedral : 7.829 48.698 350 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 7.92 % Allowed : 23.75 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.52), residues: 265 helix: 2.48 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.37 (0.67), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 248 HIS 0.001 0.000 HIS R 261 PHE 0.023 0.001 PHE L 25 TYR 0.010 0.002 TYR R 222 ARG 0.003 0.000 ARG R 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.248 Fit side-chains REVERT: R 28 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6740 (tmtm) REVERT: R 62 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8205 (p0) REVERT: R 86 CYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7027 (p) REVERT: R 216 LEU cc_start: 0.8577 (mp) cc_final: 0.8325 (mp) REVERT: R 222 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6969 (p90) REVERT: R 242 GLN cc_start: 0.8752 (pp30) cc_final: 0.8549 (pp30) outliers start: 19 outliers final: 7 residues processed: 54 average time/residue: 0.5970 time to fit residues: 33.5581 Evaluate side-chains 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 LYS Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 251 LYS Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.141116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.113752 restraints weight = 3199.445| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.73 r_work: 0.3524 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2249 Z= 0.218 Angle : 0.663 10.359 3067 Z= 0.304 Chirality : 0.045 0.308 362 Planarity : 0.003 0.037 356 Dihedral : 7.830 48.750 350 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.25 % Allowed : 28.75 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.52), residues: 265 helix: 2.53 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -2.37 (0.66), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 248 HIS 0.001 0.001 HIS R 261 PHE 0.030 0.001 PHE L 25 TYR 0.011 0.002 TYR R 222 ARG 0.003 0.000 ARG R 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.224 Fit side-chains REVERT: R 28 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6778 (tmtm) REVERT: R 222 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.6988 (p90) REVERT: R 242 GLN cc_start: 0.8739 (pp30) cc_final: 0.8528 (pp30) REVERT: R 250 TRP cc_start: 0.7348 (OUTLIER) cc_final: 0.6682 (m-90) outliers start: 15 outliers final: 10 residues processed: 48 average time/residue: 0.6730 time to fit residues: 33.5859 Evaluate side-chains 55 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 LYS Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 250 TRP Chi-restraints excluded: chain R residue 251 LYS Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.0470 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.143975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.116615 restraints weight = 3215.667| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.78 r_work: 0.3546 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2249 Z= 0.175 Angle : 0.628 8.676 3067 Z= 0.290 Chirality : 0.043 0.304 362 Planarity : 0.003 0.037 356 Dihedral : 7.839 49.489 350 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 7.08 % Allowed : 28.33 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.53), residues: 265 helix: 2.60 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.46 (0.67), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 248 HIS 0.001 0.000 HIS R 261 PHE 0.017 0.001 PHE R 183 TYR 0.010 0.002 TYR R 222 ARG 0.001 0.000 ARG R 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.237 Fit side-chains REVERT: R 222 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6916 (p90) REVERT: R 250 TRP cc_start: 0.7161 (OUTLIER) cc_final: 0.6256 (m-90) outliers start: 17 outliers final: 8 residues processed: 52 average time/residue: 0.6186 time to fit residues: 33.4861 Evaluate side-chains 52 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 250 TRP Chi-restraints excluded: chain R residue 251 LYS Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.142636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.114675 restraints weight = 3262.346| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.78 r_work: 0.3516 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2249 Z= 0.195 Angle : 0.652 9.563 3067 Z= 0.305 Chirality : 0.045 0.305 362 Planarity : 0.004 0.037 356 Dihedral : 7.803 48.790 350 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.26 % Favored : 97.36 % Rotamer: Outliers : 4.58 % Allowed : 31.67 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.53), residues: 265 helix: 2.61 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.69 (0.67), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 243 HIS 0.003 0.001 HIS R 261 PHE 0.017 0.001 PHE R 183 TYR 0.010 0.002 TYR R 222 ARG 0.007 0.001 ARG R 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: R 222 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6924 (p90) REVERT: R 250 TRP cc_start: 0.7059 (OUTLIER) cc_final: 0.6194 (m-90) REVERT: R 251 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6303 (mmtm) outliers start: 11 outliers final: 7 residues processed: 47 average time/residue: 0.6409 time to fit residues: 31.3064 Evaluate side-chains 52 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 250 TRP Chi-restraints excluded: chain R residue 251 LYS Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 0.0000 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.141304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.114234 restraints weight = 3323.614| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.83 r_work: 0.3526 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2249 Z= 0.182 Angle : 0.652 9.379 3067 Z= 0.303 Chirality : 0.045 0.305 362 Planarity : 0.003 0.037 356 Dihedral : 7.745 49.043 350 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.26 % Favored : 97.36 % Rotamer: Outliers : 4.58 % Allowed : 31.25 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.53), residues: 265 helix: 2.66 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.73 (0.67), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 243 HIS 0.002 0.001 HIS R 261 PHE 0.033 0.001 PHE L 25 TYR 0.010 0.002 TYR R 222 ARG 0.003 0.000 ARG R 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: R 201 SER cc_start: 0.8304 (m) cc_final: 0.8030 (p) REVERT: R 222 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6929 (p90) REVERT: R 250 TRP cc_start: 0.7136 (OUTLIER) cc_final: 0.6496 (m-90) REVERT: R 251 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6518 (mmtm) outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.6354 time to fit residues: 31.7586 Evaluate side-chains 53 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 250 TRP Chi-restraints excluded: chain R residue 251 LYS Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.141299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.113279 restraints weight = 3197.292| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.78 r_work: 0.3513 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2249 Z= 0.206 Angle : 0.673 9.581 3067 Z= 0.314 Chirality : 0.046 0.310 362 Planarity : 0.004 0.038 356 Dihedral : 7.656 47.943 350 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.64 % Favored : 96.98 % Rotamer: Outliers : 3.75 % Allowed : 32.50 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.53), residues: 265 helix: 2.63 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.76 (0.68), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 248 HIS 0.002 0.001 HIS R 261 PHE 0.017 0.001 PHE R 183 TYR 0.011 0.002 TYR R 222 ARG 0.007 0.001 ARG R 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: R 201 SER cc_start: 0.8280 (m) cc_final: 0.7998 (p) REVERT: R 216 LEU cc_start: 0.8624 (mp) cc_final: 0.7960 (mp) REVERT: R 222 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.6959 (p90) REVERT: R 250 TRP cc_start: 0.7113 (OUTLIER) cc_final: 0.6617 (m-90) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.5809 time to fit residues: 28.4866 Evaluate side-chains 50 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 250 TRP Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 273 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.140728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.112535 restraints weight = 3210.382| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.81 r_work: 0.3506 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2249 Z= 0.221 Angle : 0.682 9.400 3067 Z= 0.319 Chirality : 0.046 0.313 362 Planarity : 0.003 0.038 356 Dihedral : 7.597 47.415 350 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.64 % Favored : 96.98 % Rotamer: Outliers : 3.75 % Allowed : 32.50 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.53), residues: 265 helix: 2.62 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.79 (0.68), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 248 HIS 0.002 0.001 HIS R 261 PHE 0.033 0.001 PHE L 25 TYR 0.011 0.002 TYR R 222 ARG 0.003 0.000 ARG R 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1869.78 seconds wall clock time: 32 minutes 40.51 seconds (1960.51 seconds total)