Starting phenix.real_space_refine on Thu Dec 7 16:20:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/12_2023/7vv6_32139_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/12_2023/7vv6_32139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/12_2023/7vv6_32139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/12_2023/7vv6_32139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/12_2023/7vv6_32139_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/12_2023/7vv6_32139_updated.pdb" } resolution = 3.3 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 1518 2.51 5 N 342 2.21 5 O 349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "R PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 176": "OD1" <-> "OD2" Residue "R PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 254": "OD1" <-> "OD2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2227 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2227 Unusual residues: {'6IB': 1, 'CLR': 1} Classifications: {'peptide': 271, 'undetermined': 2} Link IDs: {'PTRANS': 8, 'TRANS': 262, None: 2} Not linked: pdbres="TRP R 289 " pdbres="CLR R 401 " Not linked: pdbres="CLR R 401 " pdbres="6IB R 402 " Time building chain proxies: 2.03, per 1000 atoms: 0.91 Number of scatterers: 2227 At special positions: 0 Unit cell: (65.224, 72.588, 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 349 8.00 N 342 7.00 C 1518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 258 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 0.96 Conformation dependent library (CDL) restraints added in 408.4 milliseconds 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 0 sheets defined 76.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'R' and resid 31 through 56 Processing helix chain 'R' and resid 63 through 93 removed outlier: 4.251A pdb=" N TYR R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 132 Processing helix chain 'R' and resid 134 through 138 Processing helix chain 'R' and resid 145 through 167 Processing helix chain 'R' and resid 177 through 211 removed outlier: 3.926A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 235 Processing helix chain 'R' and resid 237 through 244 Processing helix chain 'R' and resid 246 through 249 No H-bonds generated for 'chain 'R' and resid 246 through 249' Processing helix chain 'R' and resid 257 through 279 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 281 through 287 removed outlier: 4.497A pdb=" N ARG R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS R 287 " --> pdb=" O GLY R 283 " (cutoff:3.500A) 152 hydrogen bonds defined for protein. 456 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: 0.60 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 617 1.34 - 1.47: 662 1.47 - 1.59: 993 1.59 - 1.71: 1 1.71 - 1.84: 22 Bond restraints: 2295 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.669 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.28e-02 6.10e+03 6.99e+00 bond pdb=" C31 6IB R 402 " pdb=" N5 6IB R 402 " ideal model delta sigma weight residual 1.447 1.496 -0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" C32 6IB R 402 " pdb=" N6 6IB R 402 " ideal model delta sigma weight residual 1.449 1.497 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" CB VAL R 131 " pdb=" CG2 VAL R 131 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.00e+00 ... (remaining 2290 not shown) Histogram of bond angle deviations from ideal: 96.18 - 103.83: 25 103.83 - 111.48: 903 111.48 - 119.13: 970 119.13 - 126.77: 1187 126.77 - 134.42: 46 Bond angle restraints: 3131 Sorted by residual: angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 113.45 120.88 -7.43 1.39e+00 5.18e-01 2.85e+01 angle pdb=" C TRP R 250 " pdb=" N LYS R 251 " pdb=" CA LYS R 251 " ideal model delta sigma weight residual 122.08 129.29 -7.21 1.47e+00 4.63e-01 2.41e+01 angle pdb=" C GLY R 236 " pdb=" N LEU R 237 " pdb=" CA LEU R 237 " ideal model delta sigma weight residual 120.58 127.01 -6.43 1.32e+00 5.74e-01 2.37e+01 angle pdb=" CA LEU R 226 " pdb=" CB LEU R 226 " pdb=" CG LEU R 226 " ideal model delta sigma weight residual 116.30 132.37 -16.07 3.50e+00 8.16e-02 2.11e+01 angle pdb=" N SER R 177 " pdb=" CA SER R 177 " pdb=" C SER R 177 " ideal model delta sigma weight residual 111.28 115.95 -4.67 1.09e+00 8.42e-01 1.83e+01 ... (remaining 3126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.72: 1034 12.72 - 25.44: 169 25.44 - 38.16: 97 38.16 - 50.88: 34 50.88 - 63.60: 21 Dihedral angle restraints: 1355 sinusoidal: 571 harmonic: 784 Sorted by residual: dihedral pdb=" CA THR R 30 " pdb=" C THR R 30 " pdb=" N LEU R 31 " pdb=" CA LEU R 31 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP R 254 " pdb=" C ASP R 254 " pdb=" N VAL R 255 " pdb=" CA VAL R 255 " ideal model delta harmonic sigma weight residual 180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASP R 252 " pdb=" C ASP R 252 " pdb=" N SER R 253 " pdb=" CA SER R 253 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 1352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 253 0.061 - 0.122: 88 0.122 - 0.183: 23 0.183 - 0.244: 2 0.244 - 0.305: 2 Chirality restraints: 368 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C9 CLR R 401 " pdb=" C10 CLR R 401 " pdb=" C11 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.70 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA LEU R 237 " pdb=" N LEU R 237 " pdb=" C LEU R 237 " pdb=" CB LEU R 237 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 365 not shown) Planarity restraints: 361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 149 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C VAL R 149 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL R 149 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS R 150 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 43 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C VAL R 43 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL R 43 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY R 44 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 40 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C ILE R 40 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 40 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA R 41 " -0.013 2.00e-02 2.50e+03 ... (remaining 358 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 629 2.81 - 3.33: 1957 3.33 - 3.86: 3872 3.86 - 4.38: 4203 4.38 - 4.90: 7429 Nonbonded interactions: 18090 Sorted by model distance: nonbonded pdb=" O GLY R 27 " pdb=" OH TYR R 89 " model vdw 2.291 2.440 nonbonded pdb=" O SER R 264 " pdb=" OG SER R 268 " model vdw 2.306 2.440 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.320 2.440 nonbonded pdb=" O SER R 98 " pdb=" OG SER R 98 " model vdw 2.322 2.440 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.322 2.440 ... (remaining 18085 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 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: 0.180 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: 0.920 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.020 Find NCS groups from input model: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.010 0.134 2295 Z= 0.587 Angle : 1.380 16.073 3131 Z= 0.707 Chirality : 0.068 0.305 368 Planarity : 0.009 0.048 361 Dihedral : 19.052 63.599 841 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 10.37 % Allowed : 24.90 % Favored : 64.73 % 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: -4.22 (0.34), residues: 269 helix: -2.49 (0.23), residues: 208 sheet: None (None), residues: 0 loop : -3.08 (0.63), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP R 289 HIS 0.004 0.001 HIS R 261 PHE 0.020 0.003 PHE R 183 TYR 0.021 0.004 TYR R 89 ARG 0.005 0.001 ARG R 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 49 time to evaluate : 0.244 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 67 average time/residue: 0.1205 time to fit residues: 9.6898 Evaluate side-chains 30 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.240 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0245 time to fit residues: 0.3559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 275 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2295 Z= 0.160 Angle : 0.618 9.114 3131 Z= 0.295 Chirality : 0.041 0.201 368 Planarity : 0.004 0.032 361 Dihedral : 10.381 55.603 379 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.32 % Allowed : 27.39 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.49), residues: 269 helix: 0.69 (0.33), residues: 211 sheet: None (None), residues: 0 loop : -2.28 (0.77), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 248 HIS 0.001 0.000 HIS R 259 PHE 0.008 0.001 PHE R 183 TYR 0.010 0.001 TYR R 222 ARG 0.006 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.365 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 42 average time/residue: 0.1308 time to fit residues: 6.8299 Evaluate side-chains 35 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.236 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0265 time to fit residues: 0.4681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.0470 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2295 Z= 0.155 Angle : 0.560 5.999 3131 Z= 0.268 Chirality : 0.039 0.147 368 Planarity : 0.003 0.031 361 Dihedral : 8.928 57.815 379 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.24 % Allowed : 26.97 % Favored : 71.78 % 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: 1.59 (0.51), residues: 269 helix: 1.89 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -2.07 (0.77), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 243 HIS 0.001 0.000 HIS R 144 PHE 0.007 0.001 PHE R 183 TYR 0.008 0.001 TYR R 279 ARG 0.002 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.254 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.1334 time to fit residues: 6.0258 Evaluate side-chains 32 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.247 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0265 time to fit residues: 0.3693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.0170 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2295 Z= 0.141 Angle : 0.517 5.917 3131 Z= 0.249 Chirality : 0.039 0.160 368 Planarity : 0.003 0.030 361 Dihedral : 8.691 55.927 379 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.07 % Allowed : 27.80 % Favored : 70.12 % 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: 2.15 (0.52), residues: 269 helix: 2.23 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -2.16 (0.79), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.006 0.001 PHE R 280 TYR 0.009 0.001 TYR R 222 ARG 0.001 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.281 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 40 average time/residue: 0.1252 time to fit residues: 6.1250 Evaluate side-chains 34 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.247 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0241 time to fit residues: 0.3603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2295 Z= 0.170 Angle : 0.523 6.064 3131 Z= 0.250 Chirality : 0.039 0.154 368 Planarity : 0.003 0.029 361 Dihedral : 8.765 58.159 379 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.83 % Allowed : 28.63 % Favored : 70.54 % 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: 2.59 (0.53), residues: 269 helix: 2.54 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -1.68 (0.82), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.007 0.001 PHE R 280 TYR 0.011 0.001 TYR R 279 ARG 0.002 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.237 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.1174 time to fit residues: 4.8787 Evaluate side-chains 33 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0268 time to fit residues: 0.4295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2295 Z= 0.323 Angle : 0.593 6.940 3131 Z= 0.286 Chirality : 0.043 0.184 368 Planarity : 0.003 0.029 361 Dihedral : 9.791 57.736 379 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.24 % Allowed : 29.05 % Favored : 69.71 % 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: 2.52 (0.53), residues: 269 helix: 2.46 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -1.55 (0.85), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 250 HIS 0.002 0.001 HIS R 261 PHE 0.012 0.001 PHE R 167 TYR 0.014 0.002 TYR R 279 ARG 0.001 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.277 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.1379 time to fit residues: 5.5705 Evaluate side-chains 31 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.245 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0263 time to fit residues: 0.4126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.0020 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2295 Z= 0.163 Angle : 0.531 6.005 3131 Z= 0.257 Chirality : 0.039 0.153 368 Planarity : 0.003 0.028 361 Dihedral : 8.603 55.952 379 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 31.54 % Favored : 68.46 % 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: 2.87 (0.53), residues: 269 helix: 2.76 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.59 (0.83), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.008 0.001 PHE R 183 TYR 0.009 0.001 TYR R 279 ARG 0.001 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.260 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1151 time to fit residues: 5.1608 Evaluate side-chains 34 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.226 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2295 Z= 0.172 Angle : 0.542 6.018 3131 Z= 0.264 Chirality : 0.039 0.159 368 Planarity : 0.003 0.028 361 Dihedral : 8.359 55.648 379 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.83 % Allowed : 31.12 % Favored : 68.05 % 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: 2.94 (0.53), residues: 269 helix: 2.83 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.63 (0.81), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.007 0.001 PHE R 183 TYR 0.010 0.001 TYR R 279 ARG 0.001 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.249 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.1432 time to fit residues: 6.8695 Evaluate side-chains 40 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.243 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0265 time to fit residues: 0.3665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2295 Z= 0.195 Angle : 0.555 6.100 3131 Z= 0.270 Chirality : 0.040 0.157 368 Planarity : 0.003 0.028 361 Dihedral : 8.246 55.075 379 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.41 % Allowed : 31.54 % Favored : 68.05 % 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: 2.99 (0.53), residues: 269 helix: 2.85 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.55 (0.82), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 243 HIS 0.001 0.001 HIS R 261 PHE 0.007 0.001 PHE R 183 TYR 0.010 0.002 TYR R 279 ARG 0.002 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.272 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.1226 time to fit residues: 5.8512 Evaluate side-chains 37 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.249 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2295 Z= 0.193 Angle : 0.557 6.066 3131 Z= 0.273 Chirality : 0.040 0.158 368 Planarity : 0.003 0.028 361 Dihedral : 8.085 54.730 379 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.41 % Allowed : 32.78 % Favored : 66.80 % 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: 3.03 (0.53), residues: 269 helix: 2.88 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.53 (0.82), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 243 HIS 0.001 0.001 HIS R 261 PHE 0.007 0.001 PHE R 183 TYR 0.011 0.002 TYR R 279 ARG 0.002 0.000 ARG R 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.251 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.1260 time to fit residues: 5.7545 Evaluate side-chains 37 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.251 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 25 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.082290 restraints weight = 3716.791| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.24 r_work: 0.2839 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2295 Z= 0.162 Angle : 0.539 5.900 3131 Z= 0.263 Chirality : 0.039 0.166 368 Planarity : 0.003 0.028 361 Dihedral : 7.658 53.477 379 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 33.20 % Favored : 66.80 % 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: 3.05 (0.53), residues: 269 helix: 3.02 (0.36), residues: 207 sheet: None (None), residues: 0 loop : -1.76 (0.77), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 243 HIS 0.000 0.000 HIS R 144 PHE 0.006 0.001 PHE R 183 TYR 0.009 0.001 TYR R 279 ARG 0.002 0.000 ARG R 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 903.57 seconds wall clock time: 17 minutes 6.30 seconds (1026.30 seconds total)