Starting phenix.real_space_refine on Thu Dec 7 16:15:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv0_32133/12_2023/7vv0_32133_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv0_32133/12_2023/7vv0_32133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv0_32133/12_2023/7vv0_32133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv0_32133/12_2023/7vv0_32133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv0_32133/12_2023/7vv0_32133_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv0_32133/12_2023/7vv0_32133_updated.pdb" } resolution = 3.5 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 1477 2.51 5 N 340 2.21 5 O 340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 10": "NH1" <-> "NH2" Residue "R GLU 29": "OE1" <-> "OE2" Residue "R ASP 75": "OD1" <-> "OD2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "R ARG 143": "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 ASP 184": "OD1" <-> "OD2" Residue "R PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2175 Number of models: 1 Model: "" Number of chains: 2 Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "R" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2121 Unusual residues: {'CLR': 1} Classifications: {'peptide': 263, 'undetermined': 1} Link IDs: {'PTRANS': 8, 'TRANS': 254, None: 1} Not linked: pdbres="GLN R 288 " pdbres="CLR R 401 " Time building chain proxies: 1.83, per 1000 atoms: 0.84 Number of scatterers: 2175 At special positions: 0 Unit cell: (65.4594, 72.0882, 61.3164, 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 340 8.00 N 340 7.00 C 1477 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=2.03 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 395.0 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 502 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'R' and resid 31 through 57 removed outlier: 3.566A pdb=" N LEU R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 93 Processing helix chain 'R' and resid 104 through 132 removed outlier: 3.865A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 146 through 159 Processing helix chain 'R' and resid 162 through 168 removed outlier: 4.367A pdb=" N PHE R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 212 removed outlier: 3.992A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 234 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 273 Proline residue: R 262 - end of helix Processing helix chain 'R' and resid 275 through 279 146 hydrogen bonds defined for protein. 438 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: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 299 1.29 - 1.42: 660 1.42 - 1.55: 1251 1.55 - 1.68: 9 1.68 - 1.81: 22 Bond restraints: 2241 Sorted by residual: bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.426 -0.090 1.36e-02 5.41e+03 4.39e+01 bond pdb=" C LEU R 38 " pdb=" O LEU R 38 " ideal model delta sigma weight residual 1.236 1.157 0.080 1.32e-02 5.74e+03 3.64e+01 bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.619 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N TRP R 179 " pdb=" CA TRP R 179 " ideal model delta sigma weight residual 1.458 1.406 0.052 1.30e-02 5.92e+03 1.62e+01 bond pdb=" C TRP R 179 " pdb=" O TRP R 179 " ideal model delta sigma weight residual 1.233 1.174 0.059 1.53e-02 4.27e+03 1.48e+01 ... (remaining 2236 not shown) Histogram of bond angle deviations from ideal: 94.28 - 102.23: 6 102.23 - 110.19: 484 110.19 - 118.15: 1212 118.15 - 126.11: 1295 126.11 - 134.06: 57 Bond angle restraints: 3054 Sorted by residual: angle pdb=" N ARG R 286 " pdb=" CA ARG R 286 " pdb=" C ARG R 286 " ideal model delta sigma weight residual 111.28 123.19 -11.91 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N SER R 284 " pdb=" CA SER R 284 " pdb=" C SER R 284 " ideal model delta sigma weight residual 112.30 122.92 -10.62 1.36e+00 5.41e-01 6.10e+01 angle pdb=" N TRP R 179 " pdb=" CA TRP R 179 " pdb=" C TRP R 179 " ideal model delta sigma weight residual 113.55 104.34 9.21 1.26e+00 6.30e-01 5.34e+01 angle pdb=" N LYS L 11 " pdb=" CA LYS L 11 " pdb=" C LYS L 11 " ideal model delta sigma weight residual 107.93 119.23 -11.30 1.65e+00 3.67e-01 4.69e+01 angle pdb=" C PHE R 285 " pdb=" N ARG R 286 " pdb=" CA ARG R 286 " ideal model delta sigma weight residual 120.28 127.44 -7.16 1.34e+00 5.57e-01 2.85e+01 ... (remaining 3049 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 11.66: 1071 11.66 - 23.31: 162 23.31 - 34.96: 59 34.96 - 46.61: 20 46.61 - 58.26: 9 Dihedral angle restraints: 1321 sinusoidal: 547 harmonic: 774 Sorted by residual: dihedral pdb=" CB CYS R 26 " pdb=" SG CYS R 26 " pdb=" SG CYS R 258 " pdb=" CB CYS R 258 " ideal model delta sinusoidal sigma weight residual 93.00 151.26 -58.26 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CA GLU R 164 " pdb=" C GLU R 164 " pdb=" N GLY R 165 " pdb=" CA GLY R 165 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C ILE R 32 " pdb=" N ILE R 32 " pdb=" CA ILE R 32 " pdb=" CB ILE R 32 " ideal model delta harmonic sigma weight residual -122.00 -132.39 10.39 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 1318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 342 0.151 - 0.303: 14 0.303 - 0.454: 3 0.454 - 0.605: 1 0.605 - 0.757: 1 Chirality restraints: 361 Sorted by residual: chirality pdb=" CB ILE R 32 " pdb=" CA ILE R 32 " pdb=" CG1 ILE R 32 " pdb=" CG2 ILE R 32 " both_signs ideal model delta sigma weight residual False 2.64 1.89 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA SER R 284 " pdb=" N SER R 284 " pdb=" C SER R 284 " pdb=" CB SER R 284 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.78e+00 chirality pdb=" CA ARG R 286 " pdb=" N ARG R 286 " pdb=" C ARG R 286 " pdb=" CB ARG R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.66e+00 ... (remaining 358 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 37 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C ILE R 37 " 0.069 2.00e-02 2.50e+03 pdb=" O ILE R 37 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU R 38 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 149 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C VAL R 149 " -0.066 2.00e-02 2.50e+03 pdb=" O VAL R 149 " 0.025 2.00e-02 2.50e+03 pdb=" N CYS R 150 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 151 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C VAL R 151 " 0.063 2.00e-02 2.50e+03 pdb=" O VAL R 151 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU R 152 " -0.021 2.00e-02 2.50e+03 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 17 2.59 - 3.16: 1683 3.16 - 3.74: 3462 3.74 - 4.32: 4528 4.32 - 4.90: 7434 Nonbonded interactions: 17124 Sorted by model distance: nonbonded pdb=" CD1 LEU R 38 " pdb=" CD1 ILE R 83 " model vdw 2.007 3.880 nonbonded pdb=" O LYS L 12 " pdb=" CE1 PHE R 257 " model vdw 2.215 3.340 nonbonded pdb=" CZ2 TRP L 13 " pdb=" CH2 TRP R 243 " model vdw 2.304 3.640 nonbonded pdb=" NH1 ARG L 10 " pdb=" OD2 ASP R 184 " model vdw 2.311 2.520 nonbonded pdb=" O SER R 284 " pdb=" OG SER R 284 " model vdw 2.317 2.440 ... (remaining 17119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.340 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: 1.760 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.720 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 0.090 2241 Z= 0.613 Angle : 1.491 15.143 3054 Z= 0.808 Chirality : 0.091 0.757 361 Planarity : 0.012 0.083 354 Dihedral : 14.054 56.619 813 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.93 % Allowed : 1.67 % Favored : 95.40 % Cbeta Deviations : 0.40 % 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: -3.44 (0.39), residues: 264 helix: -2.01 (0.28), residues: 205 sheet: None (None), residues: 0 loop : -2.48 (0.60), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 243 HIS 0.004 0.001 HIS R 261 PHE 0.028 0.003 PHE R 244 TYR 0.012 0.003 TYR R 279 ARG 0.027 0.002 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.236 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 0.2416 time to fit residues: 8.1534 Evaluate side-chains 26 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.177 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1096 time to fit residues: 1.0509 ------------------------------------------------------------------------------- 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: 0.6980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 GLN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2241 Z= 0.215 Angle : 0.665 7.666 3054 Z= 0.326 Chirality : 0.045 0.339 361 Planarity : 0.006 0.046 354 Dihedral : 7.416 48.086 350 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.67 % Allowed : 10.46 % Favored : 87.87 % 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: -0.34 (0.49), residues: 264 helix: 0.32 (0.34), residues: 210 sheet: None (None), residues: 0 loop : -2.09 (0.74), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 154 HIS 0.001 0.001 HIS R 261 PHE 0.014 0.001 PHE R 244 TYR 0.005 0.001 TYR R 113 ARG 0.005 0.001 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.234 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.2059 time to fit residues: 7.1402 Evaluate side-chains 26 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.240 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0318 time to fit residues: 0.4893 ------------------------------------------------------------------------------- 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: 1.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 19 optimal weight: 0.1980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2241 Z= 0.164 Angle : 0.585 6.103 3054 Z= 0.281 Chirality : 0.044 0.318 361 Planarity : 0.004 0.039 354 Dihedral : 6.994 55.528 350 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.51 % Allowed : 11.72 % Favored : 85.77 % 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: 1.11 (0.52), residues: 264 helix: 1.38 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.78 (0.75), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 133 HIS 0.000 0.000 HIS R 261 PHE 0.008 0.001 PHE R 244 TYR 0.007 0.001 TYR R 113 ARG 0.005 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.259 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 32 average time/residue: 0.1884 time to fit residues: 7.0427 Evaluate side-chains 27 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.237 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0391 time to fit residues: 0.5159 ------------------------------------------------------------------------------- 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: 0.7980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2241 Z= 0.212 Angle : 0.576 6.289 3054 Z= 0.282 Chirality : 0.042 0.325 361 Planarity : 0.004 0.036 354 Dihedral : 6.787 52.409 350 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.09 % Allowed : 15.90 % Favored : 82.01 % 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: 1.42 (0.52), residues: 264 helix: 1.57 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.56 (0.76), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 190 HIS 0.000 0.000 HIS R 259 PHE 0.016 0.001 PHE R 257 TYR 0.006 0.001 TYR R 113 ARG 0.005 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.228 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.1949 time to fit residues: 6.5885 Evaluate side-chains 29 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.239 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0291 time to fit residues: 0.5244 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2241 Z= 0.149 Angle : 0.540 7.017 3054 Z= 0.259 Chirality : 0.039 0.297 361 Planarity : 0.004 0.033 354 Dihedral : 6.337 53.777 350 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.67 % Allowed : 16.74 % Favored : 81.59 % 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: 1.83 (0.53), residues: 264 helix: 1.87 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.42 (0.77), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 133 HIS 0.000 0.000 HIS R 259 PHE 0.016 0.001 PHE R 257 TYR 0.007 0.001 TYR R 113 ARG 0.006 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.230 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 22 average time/residue: 0.1937 time to fit residues: 5.0672 Evaluate side-chains 22 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.233 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0267 time to fit residues: 0.3787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2241 Z= 0.203 Angle : 0.573 6.287 3054 Z= 0.277 Chirality : 0.041 0.304 361 Planarity : 0.004 0.031 354 Dihedral : 6.412 54.293 350 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.35 % Allowed : 17.99 % Favored : 78.66 % 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: 1.73 (0.52), residues: 264 helix: 1.77 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -1.34 (0.78), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 190 HIS 0.001 0.000 HIS R 259 PHE 0.013 0.001 PHE R 257 TYR 0.007 0.001 TYR R 113 ARG 0.005 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.215 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 30 average time/residue: 0.1970 time to fit residues: 6.8148 Evaluate side-chains 30 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.242 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0243 time to fit residues: 0.4790 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.0070 chunk 24 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2241 Z= 0.170 Angle : 0.550 5.772 3054 Z= 0.265 Chirality : 0.040 0.285 361 Planarity : 0.004 0.030 354 Dihedral : 6.391 57.279 350 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.67 % Allowed : 19.25 % Favored : 79.08 % 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: 1.92 (0.53), residues: 264 helix: 1.93 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.39 (0.78), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 243 HIS 0.000 0.000 HIS R 259 PHE 0.012 0.001 PHE R 257 TYR 0.007 0.001 TYR R 113 ARG 0.006 0.001 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.227 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 0.1911 time to fit residues: 6.9000 Evaluate side-chains 28 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.235 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0425 time to fit residues: 0.3921 ------------------------------------------------------------------------------- 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: 0.9990 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 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: 0.7787 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2241 Z= 0.199 Angle : 0.566 5.526 3054 Z= 0.275 Chirality : 0.041 0.292 361 Planarity : 0.004 0.030 354 Dihedral : 6.452 56.906 350 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.51 % Allowed : 20.08 % Favored : 77.41 % 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: 1.79 (0.53), residues: 264 helix: 1.84 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -1.45 (0.79), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 243 HIS 0.001 0.000 HIS R 259 PHE 0.010 0.001 PHE R 257 TYR 0.008 0.001 TYR R 113 ARG 0.006 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.236 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 31 average time/residue: 0.1940 time to fit residues: 6.9845 Evaluate side-chains 31 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.236 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0326 time to fit residues: 0.4837 ------------------------------------------------------------------------------- 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: 0.0170 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 3 optimal weight: 0.5980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2241 Z= 0.133 Angle : 0.515 5.398 3054 Z= 0.251 Chirality : 0.038 0.244 361 Planarity : 0.004 0.030 354 Dihedral : 6.295 57.947 350 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.42 % Allowed : 21.34 % Favored : 78.24 % 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: 1.98 (0.54), residues: 264 helix: 1.95 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -1.82 (0.83), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 243 HIS 0.000 0.000 HIS R 261 PHE 0.022 0.001 PHE R 257 TYR 0.008 0.001 TYR R 113 ARG 0.006 0.001 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.238 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.2282 time to fit residues: 6.3461 Evaluate side-chains 21 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.251 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3291 ------------------------------------------------------------------------------- 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: 1.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7757 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 0.031 2241 Z= 0.180 Angle : 0.545 5.465 3054 Z= 0.266 Chirality : 0.040 0.261 361 Planarity : 0.004 0.032 354 Dihedral : 6.419 59.427 350 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.26 % Allowed : 22.18 % Favored : 76.57 % 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: 1.91 (0.54), residues: 264 helix: 1.89 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -1.75 (0.84), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 190 HIS 0.000 0.000 HIS R 259 PHE 0.019 0.001 PHE R 257 TYR 0.008 0.001 TYR R 279 ARG 0.006 0.000 ARG R 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.244 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 23 average time/residue: 0.2300 time to fit residues: 6.1246 Evaluate side-chains 22 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.236 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3370 ------------------------------------------------------------------------------- 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: 0.6980 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.170528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143952 restraints weight = 2313.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147606 restraints weight = 1370.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150198 restraints weight = 1019.979| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2241 Z= 0.190 Angle : 0.555 5.500 3054 Z= 0.270 Chirality : 0.040 0.263 361 Planarity : 0.004 0.032 354 Dihedral : 6.395 58.603 350 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.09 % Allowed : 21.76 % Favored : 76.15 % 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: 1.90 (0.53), residues: 264 helix: 1.91 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -1.45 (0.79), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 190 HIS 0.000 0.000 HIS R 144 PHE 0.019 0.001 PHE R 257 TYR 0.008 0.001 TYR R 279 ARG 0.007 0.000 ARG R 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 899.84 seconds wall clock time: 17 minutes 19.60 seconds (1039.60 seconds total)