Starting phenix.real_space_refine (version: dev) on Mon Apr 4 11:25:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/04_2022/7vv6_32139_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/04_2022/7vv6_32139.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/04_2022/7vv6_32139_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/04_2022/7vv6_32139_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/04_2022/7vv6_32139_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/04_2022/7vv6_32139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/04_2022/7vv6_32139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/04_2022/7vv6_32139_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv6_32139/04_2022/7vv6_32139_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-dev-4553/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: {'undetermined': 2, 'peptide': 271} 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: 2.18, per 1000 atoms: 0.98 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: 1.14 Conformation dependent library (CDL) restraints added in 341.1 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: 0.23 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: 0.58 Time building geometry restraints manager: 1.24 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=" C32 6IB R 402 " pdb=" N6 6IB R 402 " ideal model delta sigma weight residual 1.452 1.497 -0.045 2.00e-02 2.50e+03 5.09e+00 bond pdb=" C31 6IB R 402 " pdb=" N5 6IB R 402 " ideal model delta sigma weight residual 1.453 1.496 -0.043 2.00e-02 2.50e+03 4.65e+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 - 14.12: 1011 14.12 - 28.25: 171 28.25 - 42.37: 76 42.37 - 56.49: 19 56.49 - 70.61: 9 Dihedral angle restraints: 1286 sinusoidal: 502 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 1283 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 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. 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: 1.000 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 12.860 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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= 0.592 Angle : 1.434 16.073 3131 Z= 0.719 Chirality : 0.068 0.305 368 Planarity : 0.009 0.048 361 Dihedral : 18.507 70.613 772 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 % 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 : 0.288 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 67 average time/residue: 0.1145 time to fit residues: 9.2576 Evaluate side-chains 30 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.276 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0251 time to fit residues: 0.4005 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8328 moved from start: 0.2326 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= 0.158 Angle : 0.626 9.372 3131 Z= 0.296 Chirality : 0.042 0.243 368 Planarity : 0.005 0.033 361 Dihedral : 9.182 73.711 310 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 3.32 % 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: 0.64 (0.33), residues: 211 sheet: None (None), residues: 0 loop : -2.30 (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 43 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.288 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 42 average time/residue: 0.1278 time to fit residues: 6.5665 Evaluate side-chains 35 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.244 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0256 time to fit residues: 0.4941 ------------------------------------------------------------------------------- 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: 0.9980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.0040 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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: 0.8346 moved from start: 0.2871 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= 0.169 Angle : 0.567 6.858 3131 Z= 0.272 Chirality : 0.041 0.214 368 Planarity : 0.003 0.031 361 Dihedral : 8.169 69.178 310 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 1.66 % 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: 1.58 (0.52), residues: 269 helix: 1.88 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -2.03 (0.78), 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 39 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.265 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.1304 time to fit residues: 5.9291 Evaluate side-chains 34 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.266 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0253 time to fit residues: 0.4497 ------------------------------------------------------------------------------- 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: 0.0870 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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: 0.8345 moved from start: 0.3137 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= 0.149 Angle : 0.520 6.765 3131 Z= 0.252 Chirality : 0.039 0.203 368 Planarity : 0.003 0.030 361 Dihedral : 7.856 67.084 310 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 2.49 % 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: 2.23 (0.52), residues: 269 helix: 2.31 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -1.91 (0.80), 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 44 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.293 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 43 average time/residue: 0.1177 time to fit residues: 6.1598 Evaluate side-chains 37 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.214 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0248 time to fit residues: 0.3963 ------------------------------------------------------------------------------- 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: 5.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8358 moved from start: 0.3327 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 : 0.529 6.781 3131 Z= 0.253 Chirality : 0.040 0.202 368 Planarity : 0.003 0.029 361 Dihedral : 7.737 66.029 310 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.83 % 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: 2.50 (0.53), residues: 269 helix: 2.59 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -1.91 (0.76), residues: 61 *********************** 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 36 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.262 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.0947 time to fit residues: 4.2380 Evaluate side-chains 35 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.211 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0246 time to fit residues: 0.3600 ------------------------------------------------------------------------------- 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: 0.7980 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 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 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 2295 Z= 0.151 Angle : 0.515 6.652 3131 Z= 0.247 Chirality : 0.039 0.192 368 Planarity : 0.003 0.028 361 Dihedral : 7.544 64.866 310 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.41 % 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: 2.88 (0.53), residues: 269 helix: 2.77 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.62 (0.82), residues: 58 *********************** 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 39 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.268 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.1302 time to fit residues: 6.0519 Evaluate side-chains 37 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.267 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3808 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8360 moved from start: 0.3620 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= 0.166 Angle : 0.526 6.696 3131 Z= 0.252 Chirality : 0.039 0.192 368 Planarity : 0.003 0.028 361 Dihedral : 7.501 64.642 310 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.83 % 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: 2.97 (0.53), residues: 269 helix: 2.81 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -1.53 (0.83), residues: 57 *********************** 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 41 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.269 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.1374 time to fit residues: 6.6941 Evaluate side-chains 37 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0271 time to fit residues: 0.4084 ------------------------------------------------------------------------------- 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: 1.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8355 moved from start: 0.3773 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= 0.178 Angle : 0.541 6.730 3131 Z= 0.261 Chirality : 0.040 0.195 368 Planarity : 0.003 0.028 361 Dihedral : 7.489 64.462 310 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.66 % 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: 3.08 (0.53), residues: 269 helix: 2.88 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -1.48 (0.84), residues: 57 *********************** 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 40 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.270 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 39 average time/residue: 0.1250 time to fit residues: 6.0382 Evaluate side-chains 37 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0279 time to fit residues: 0.4307 ------------------------------------------------------------------------------- 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: 0.5980 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.8343 moved from start: 0.3890 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= 0.163 Angle : 0.538 6.582 3131 Z= 0.261 Chirality : 0.039 0.185 368 Planarity : 0.003 0.029 361 Dihedral : 7.439 63.990 310 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.41 % 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: 3.06 (0.53), residues: 269 helix: 2.91 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.59 (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 42 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.274 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.1377 time to fit residues: 6.8361 Evaluate side-chains 40 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.264 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3462 ------------------------------------------------------------------------------- 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: 0.8980 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8350 moved from start: 0.3933 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= 0.174 Angle : 0.543 6.584 3131 Z= 0.265 Chirality : 0.039 0.184 368 Planarity : 0.003 0.028 361 Dihedral : 7.414 63.741 310 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.41 % 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: 3.08 (0.53), residues: 269 helix: 2.91 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.52 (0.84), 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 40 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.279 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.1223 time to fit residues: 5.9248 Evaluate side-chains 39 residues out of total 241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.286 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0311 time to fit residues: 0.4133 ------------------------------------------------------------------------------- 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: 0.6980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.107443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.081256 restraints weight = 3707.968| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.28 r_work: 0.2943 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work: 0.2919 rms_B_bonded: 2.09 restraints_weight: 0.1250 r_work: 0.2907 rms_B_bonded: 2.15 restraints_weight: 0.0625 r_work: 0.2895 rms_B_bonded: 2.24 restraints_weight: 0.0312 r_work: 0.2882 rms_B_bonded: 2.35 restraints_weight: 0.0156 r_work: 0.2868 rms_B_bonded: 2.48 restraints_weight: 0.0078 r_work: 0.2854 rms_B_bonded: 2.64 restraints_weight: 0.0039 r_work: 0.2840 rms_B_bonded: 2.82 restraints_weight: 0.0020 r_work: 0.2824 rms_B_bonded: 3.02 restraints_weight: 0.0010 r_work: 0.2808 rms_B_bonded: 3.25 restraints_weight: 0.0005 r_work: 0.2791 rms_B_bonded: 3.50 restraints_weight: 0.0002 r_work: 0.2772 rms_B_bonded: 3.79 restraints_weight: 0.0001 r_work: 0.2753 rms_B_bonded: 4.10 restraints_weight: 0.0001 r_work: 0.2733 rms_B_bonded: 4.45 restraints_weight: 0.0000 r_work: 0.2711 rms_B_bonded: 4.83 restraints_weight: 0.0000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3979 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= 0.184 Angle : 0.549 6.616 3131 Z= 0.269 Chirality : 0.040 0.186 368 Planarity : 0.003 0.028 361 Dihedral : 7.431 63.703 310 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.53), residues: 269 helix: 2.96 (0.35), residues: 208 sheet: None (None), residues: 0 loop : -1.62 (0.80), residues: 61 =============================================================================== Job complete usr+sys time: 849.75 seconds wall clock time: 16 minutes 17.78 seconds (977.78 seconds total)