Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 17:15:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/10_2023/7vv6_32139_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/10_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_32139/10_2023/7vv6_32139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/10_2023/7vv6_32139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/10_2023/7vv6_32139_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/10_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-1.21rc1-5097/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: 1.90, per 1000 atoms: 0.85 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: 2.90 Conformation dependent library (CDL) restraints added in 984.0 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: 0.35 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: 1.00 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: 992 12.72 - 25.44: 161 25.44 - 38.16: 97 38.16 - 50.88: 32 50.88 - 63.60: 17 Dihedral angle restraints: 1299 sinusoidal: 515 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 1296 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.920 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.670 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.230 ------------------------------------------------------------------------------- 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 : 19.043 63.599 785 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 *********************** 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 : 0.264 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 67 average time/residue: 0.1217 time to fit residues: 9.8360 Evaluate side-chains 30 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.244 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0256 time to fit residues: 0.3756 ------------------------------------------------------------------------------- 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: 0.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8158 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2295 Z= 0.163 Angle : 0.621 9.131 3131 Z= 0.295 Chirality : 0.042 0.249 368 Planarity : 0.005 0.033 361 Dihedral : 9.807 55.570 323 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.32 % Allowed : 26.97 % 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: 0.02 (0.48), residues: 269 helix: 0.67 (0.33), residues: 211 sheet: None (None), residues: 0 loop : -2.28 (0.77), residues: 58 *********************** 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 42 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.251 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 40 average time/residue: 0.1325 time to fit residues: 6.4414 Evaluate side-chains 35 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.246 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0264 time to fit residues: 0.4600 ------------------------------------------------------------------------------- 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: 0.8980 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.0030 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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: 0.8165 moved from start: 0.2837 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= 0.161 Angle : 0.564 6.846 3131 Z= 0.270 Chirality : 0.040 0.212 368 Planarity : 0.003 0.031 361 Dihedral : 9.071 57.836 323 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.24 % Allowed : 27.80 % Favored : 70.95 % 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: 1.88 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -2.03 (0.77), residues: 60 *********************** 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 36 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.250 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.1399 time to fit residues: 5.9670 Evaluate side-chains 32 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.260 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0276 time to fit residues: 0.4355 ------------------------------------------------------------------------------- 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: 0.0970 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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: 0.8176 moved from start: 0.3100 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= 0.152 Angle : 0.524 6.789 3131 Z= 0.253 Chirality : 0.039 0.205 368 Planarity : 0.003 0.030 361 Dihedral : 8.824 56.272 323 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.90 % Allowed : 25.73 % Favored : 71.37 % 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: 2.22 (0.53), residues: 269 helix: 2.29 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -1.87 (0.82), residues: 57 *********************** 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 42 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.256 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 41 average time/residue: 0.1282 time to fit residues: 6.4247 Evaluate side-chains 35 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.326 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0262 time to fit residues: 0.4211 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2295 Z= 0.157 Angle : 0.520 6.763 3131 Z= 0.248 Chirality : 0.040 0.201 368 Planarity : 0.003 0.029 361 Dihedral : 8.797 57.942 323 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 29.88 % 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: 2.55 (0.53), residues: 269 helix: 2.51 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -1.67 (0.82), residues: 57 *********************** 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 31 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.263 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1166 time to fit residues: 4.5725 Evaluate side-chains 31 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.220 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2921 ------------------------------------------------------------------------------- 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: 1.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8221 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 : 0.004 0.027 2295 Z= 0.232 Angle : 0.546 6.899 3131 Z= 0.261 Chirality : 0.041 0.224 368 Planarity : 0.003 0.029 361 Dihedral : 8.881 58.695 323 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.66 % Allowed : 29.46 % Favored : 68.88 % 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: 2.70 (0.53), residues: 269 helix: 2.60 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -1.55 (0.84), residues: 57 *********************** 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 35 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.264 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.1123 time to fit residues: 5.0141 Evaluate side-chains 34 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0274 time to fit residues: 0.4924 ------------------------------------------------------------------------------- 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: 0.0570 chunk 12 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 overall best weight: 0.3298 ------------------------------------------------------------------------------- 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: 0.8167 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2295 Z= 0.128 Angle : 0.509 6.563 3131 Z= 0.242 Chirality : 0.038 0.186 368 Planarity : 0.003 0.028 361 Dihedral : 8.372 55.510 323 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 29.46 % 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: 2.98 (0.53), residues: 269 helix: 2.86 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.65 (0.81), residues: 58 *********************** 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 38 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.260 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1227 time to fit residues: 5.7786 Evaluate side-chains 34 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.252 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3325 ------------------------------------------------------------------------------- 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: 0.8980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.3614 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= 0.180 Angle : 0.534 6.724 3131 Z= 0.254 Chirality : 0.040 0.195 368 Planarity : 0.003 0.028 361 Dihedral : 8.310 55.584 323 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: 3.01 (0.53), residues: 269 helix: 2.88 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.60 (0.82), residues: 58 *********************** 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 37 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1445 time to fit residues: 6.3835 Evaluate side-chains 34 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.221 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3321 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8204 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2295 Z= 0.201 Angle : 0.543 6.923 3131 Z= 0.260 Chirality : 0.041 0.213 368 Planarity : 0.003 0.029 361 Dihedral : 8.200 55.342 323 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: 3.04 (0.53), residues: 269 helix: 2.88 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.53 (0.83), residues: 58 *********************** 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 36 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.251 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1540 time to fit residues: 6.6123 Evaluate side-chains 35 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3269 ------------------------------------------------------------------------------- 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: 2.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3843 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= 0.167 Angle : 0.541 6.755 3131 Z= 0.259 Chirality : 0.040 0.198 368 Planarity : 0.003 0.028 361 Dihedral : 7.918 54.438 323 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 31.12 % Favored : 68.88 % 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: 3.10 (0.53), residues: 269 helix: 2.92 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.50 (0.83), residues: 58 ********************** 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 34 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.261 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1561 time to fit residues: 6.3393 Evaluate side-chains 33 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3419 ------------------------------------------------------------------------------- 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: 0.8980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.105442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.080671 restraints weight = 3841.280| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.18 r_work: 0.2822 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2295 Z= 0.245 Angle : 0.580 6.954 3131 Z= 0.278 Chirality : 0.042 0.220 368 Planarity : 0.003 0.028 361 Dihedral : 8.046 55.130 323 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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: 2.94 (0.53), residues: 269 helix: 2.77 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.35 (0.83), residues: 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 886.62 seconds wall clock time: 16 minutes 39.74 seconds (999.74 seconds total)