Starting phenix.real_space_refine on Wed Nov 13 23:23:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggs_40019/11_2024/8ggs_40019.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggs_40019/11_2024/8ggs_40019.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/8ggs_40019/11_2024/8ggs_40019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggs_40019/11_2024/8ggs_40019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggs_40019/11_2024/8ggs_40019.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggs_40019/11_2024/8ggs_40019.cif" } 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= 0.023 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 15 5.16 5 C 1415 2.51 5 N 331 2.21 5 O 353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2114 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2099 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 99 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.30, per 1000 atoms: 1.09 Number of scatterers: 2114 At special positions: 0 Unit cell: (56.4005, 82.4315, 62.4744, 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 15 16.00 O 353 8.00 N 331 7.00 C 1415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 262.6 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 87.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.711A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 4.027A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 4.270A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.729A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 287 removed outlier: 3.877A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 3.618A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 318 removed outlier: 3.613A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 340 167 hydrogen bonds defined for protein. 501 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: 0.53 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 461 1.33 - 1.46: 511 1.46 - 1.58: 1177 1.58 - 1.70: 0 1.70 - 1.82: 21 Bond restraints: 2170 Sorted by residual: bond pdb=" N ARG R 151 " pdb=" CA ARG R 151 " ideal model delta sigma weight residual 1.459 1.423 0.036 1.19e-02 7.06e+03 9.18e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.452 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.574 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.442 -0.048 2.00e-02 2.50e+03 5.75e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.564 -0.044 2.00e-02 2.50e+03 4.89e+00 ... (remaining 2165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 2853 1.17 - 2.33: 98 2.33 - 3.50: 15 3.50 - 4.67: 7 4.67 - 5.83: 6 Bond angle restraints: 2979 Sorted by residual: angle pdb=" C VAL R 86 " pdb=" N VAL R 87 " pdb=" CA VAL R 87 " ideal model delta sigma weight residual 120.33 122.51 -2.18 8.00e-01 1.56e+00 7.42e+00 angle pdb=" C VAL R 87 " pdb=" CA VAL R 87 " pdb=" CB VAL R 87 " ideal model delta sigma weight residual 114.00 110.85 3.15 1.31e+00 5.83e-01 5.78e+00 angle pdb=" N ARG R 151 " pdb=" CA ARG R 151 " pdb=" C ARG R 151 " ideal model delta sigma weight residual 111.07 108.90 2.17 1.07e+00 8.73e-01 4.10e+00 angle pdb=" C THR R 96 " pdb=" N LYS R 97 " pdb=" CA LYS R 97 " ideal model delta sigma weight residual 124.31 127.60 -3.29 1.67e+00 3.59e-01 3.88e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.12 -5.49 3.00e+00 1.11e-01 3.35e+00 ... (remaining 2974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.60: 1086 12.60 - 25.19: 97 25.19 - 37.79: 43 37.79 - 50.38: 6 50.38 - 62.98: 3 Dihedral angle restraints: 1235 sinusoidal: 407 harmonic: 828 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ALA R 85 " pdb=" C ALA R 85 " pdb=" N VAL R 86 " pdb=" CA VAL R 86 " ideal model delta harmonic sigma weight residual -180.00 -164.54 -15.46 0 5.00e+00 4.00e-02 9.56e+00 dihedral pdb=" CB MET R 36 " pdb=" CG MET R 36 " pdb=" SD MET R 36 " pdb=" CE MET R 36 " ideal model delta sinusoidal sigma weight residual 60.00 117.62 -57.62 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 1232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 246 0.033 - 0.066: 89 0.066 - 0.099: 29 0.099 - 0.132: 3 0.132 - 0.165: 1 Chirality restraints: 368 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.56 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA PRO R 288 " pdb=" N PRO R 288 " pdb=" C PRO R 288 " pdb=" CB PRO R 288 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.74e-01 chirality pdb=" CA PRO R 88 " pdb=" N PRO R 88 " pdb=" C PRO R 88 " pdb=" CB PRO R 88 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.62e-01 ... (remaining 365 not shown) Planarity restraints: 357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO R 168 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.016 5.00e-02 4.00e+02 2.47e-02 9.75e-01 pdb=" N PRO R 211 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 287 " -0.016 5.00e-02 4.00e+02 2.41e-02 9.27e-01 pdb=" N PRO R 288 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO R 288 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 288 " -0.014 5.00e-02 4.00e+02 ... (remaining 354 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 562 2.81 - 3.34: 2166 3.34 - 3.86: 3342 3.86 - 4.38: 3425 4.38 - 4.90: 6406 Nonbonded interactions: 15901 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.317 3.040 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.505 3.040 nonbonded pdb=" OD1 ASN R 196 " pdb=" N GLN R 197 " model vdw 2.594 3.120 nonbonded pdb=" OG SER R 165 " pdb=" N PHE R 166 " model vdw 2.625 3.120 ... (remaining 15896 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=0.00 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: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.660 Find NCS groups from input model: 0.020 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.004 0.055 2170 Z= 0.265 Angle : 0.562 5.833 2979 Z= 0.317 Chirality : 0.038 0.165 368 Planarity : 0.004 0.044 357 Dihedral : 12.384 62.978 694 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.50), residues: 277 helix: 2.47 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.62 (0.71), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.002 0.001 HIS R 296 PHE 0.007 0.001 PHE R 133 TYR 0.010 0.001 TYR R 70 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.230 Fit side-chains REVERT: R 63 ARG cc_start: 0.7022 (mtm180) cc_final: 0.5599 (mpt180) REVERT: R 84 LEU cc_start: 0.8143 (mm) cc_final: 0.7740 (mm) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2085 time to fit residues: 7.6012 Evaluate side-chains 24 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.0050 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 14 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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: 0.7930 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2170 Z= 0.159 Angle : 0.466 4.849 2979 Z= 0.258 Chirality : 0.038 0.110 368 Planarity : 0.003 0.026 357 Dihedral : 4.257 18.022 309 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.94 % Allowed : 10.19 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.50), residues: 277 helix: 2.55 (0.34), residues: 222 sheet: None (None), residues: 0 loop : -2.21 (0.68), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 282 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.224 Fit side-chains REVERT: R 63 ARG cc_start: 0.7188 (mtm180) cc_final: 0.5671 (mpt180) REVERT: R 84 LEU cc_start: 0.8198 (mm) cc_final: 0.7664 (mm) REVERT: R 151 ARG cc_start: 0.7518 (mtm-85) cc_final: 0.6492 (mmt-90) REVERT: R 205 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7607 (mp) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 0.1873 time to fit residues: 7.3395 Evaluate side-chains 30 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 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 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2170 Z= 0.206 Angle : 0.474 5.211 2979 Z= 0.264 Chirality : 0.039 0.114 368 Planarity : 0.003 0.027 357 Dihedral : 4.420 17.864 309 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.37 % Allowed : 13.11 % Favored : 82.52 % 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: 2.67 (0.50), residues: 277 helix: 2.72 (0.34), residues: 220 sheet: None (None), residues: 0 loop : -2.36 (0.64), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 313 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 282 TYR 0.007 0.001 TYR R 308 ARG 0.002 0.000 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.7441 (mtm180) cc_final: 0.5710 (mpt180) REVERT: R 84 LEU cc_start: 0.8202 (mm) cc_final: 0.7623 (mm) REVERT: R 205 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7624 (mp) outliers start: 9 outliers final: 7 residues processed: 31 average time/residue: 0.1956 time to fit residues: 6.9833 Evaluate side-chains 30 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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: 0.7992 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2170 Z= 0.177 Angle : 0.457 5.260 2979 Z= 0.255 Chirality : 0.038 0.112 368 Planarity : 0.003 0.027 357 Dihedral : 4.355 17.710 309 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.40 % Allowed : 15.05 % Favored : 81.55 % 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: 2.68 (0.50), residues: 277 helix: 2.76 (0.34), residues: 220 sheet: None (None), residues: 0 loop : -2.49 (0.63), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 313 HIS 0.004 0.001 HIS R 296 PHE 0.008 0.001 PHE R 282 TYR 0.006 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.7457 (mtm180) cc_final: 0.5655 (mpt180) REVERT: R 84 LEU cc_start: 0.8197 (mm) cc_final: 0.7590 (mm) REVERT: R 151 ARG cc_start: 0.7427 (mtm-85) cc_final: 0.6455 (mmt-90) REVERT: R 205 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7597 (mp) outliers start: 7 outliers final: 6 residues processed: 32 average time/residue: 0.1972 time to fit residues: 7.2634 Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.0170 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2170 Z= 0.163 Angle : 0.436 5.281 2979 Z= 0.244 Chirality : 0.037 0.110 368 Planarity : 0.003 0.027 357 Dihedral : 4.274 17.658 309 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.40 % Allowed : 15.53 % Favored : 81.07 % 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: 2.77 (0.50), residues: 277 helix: 2.80 (0.34), residues: 221 sheet: None (None), residues: 0 loop : -2.49 (0.62), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.002 0.001 HIS R 93 PHE 0.008 0.001 PHE R 282 TYR 0.007 0.001 TYR R 308 ARG 0.001 0.000 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.7497 (mtm180) cc_final: 0.5700 (mmt180) REVERT: R 84 LEU cc_start: 0.8175 (mm) cc_final: 0.7579 (mm) REVERT: R 151 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.6453 (mmt-90) REVERT: R 205 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7634 (mp) outliers start: 7 outliers final: 5 residues processed: 31 average time/residue: 0.1956 time to fit residues: 6.9779 Evaluate side-chains 29 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 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 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2170 Z= 0.205 Angle : 0.465 5.315 2979 Z= 0.262 Chirality : 0.038 0.116 368 Planarity : 0.003 0.027 357 Dihedral : 4.358 17.731 309 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.88 % Allowed : 19.42 % Favored : 76.70 % 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: 2.74 (0.50), residues: 277 helix: 2.84 (0.34), residues: 219 sheet: None (None), residues: 0 loop : -2.57 (0.60), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.009 0.001 PHE R 282 TYR 0.007 0.001 TYR R 308 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.7632 (mtm180) cc_final: 0.5780 (mmt180) REVERT: R 84 LEU cc_start: 0.8201 (mm) cc_final: 0.7584 (mm) REVERT: R 151 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.6468 (mmt-90) REVERT: R 205 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7636 (mp) outliers start: 8 outliers final: 5 residues processed: 33 average time/residue: 0.1896 time to fit residues: 7.1841 Evaluate side-chains 31 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 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: 0.8035 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2170 Z= 0.223 Angle : 0.475 5.333 2979 Z= 0.268 Chirality : 0.039 0.114 368 Planarity : 0.003 0.028 357 Dihedral : 4.381 17.726 309 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.37 % Allowed : 19.90 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.50), residues: 277 helix: 2.84 (0.34), residues: 219 sheet: None (None), residues: 0 loop : -2.55 (0.61), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.009 0.001 PHE R 282 TYR 0.008 0.001 TYR R 308 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.7676 (mtm180) cc_final: 0.5871 (mmt180) REVERT: R 84 LEU cc_start: 0.8205 (mm) cc_final: 0.7588 (mm) REVERT: R 151 ARG cc_start: 0.7388 (mtm-85) cc_final: 0.6463 (mmt-90) REVERT: R 205 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7637 (mp) outliers start: 9 outliers final: 5 residues processed: 32 average time/residue: 0.1812 time to fit residues: 6.7069 Evaluate side-chains 31 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2170 Z= 0.218 Angle : 0.472 5.323 2979 Z= 0.266 Chirality : 0.039 0.114 368 Planarity : 0.003 0.028 357 Dihedral : 4.401 17.882 309 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.37 % Allowed : 20.39 % Favored : 75.24 % 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: 2.68 (0.50), residues: 277 helix: 2.78 (0.34), residues: 219 sheet: None (None), residues: 0 loop : -2.53 (0.62), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.002 0.001 HIS R 178 PHE 0.009 0.001 PHE R 282 TYR 0.008 0.001 TYR R 308 ARG 0.002 0.001 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.7740 (mtm180) cc_final: 0.5926 (mmt180) REVERT: R 84 LEU cc_start: 0.8220 (mm) cc_final: 0.7613 (mm) REVERT: R 205 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7664 (mp) outliers start: 9 outliers final: 5 residues processed: 32 average time/residue: 0.2082 time to fit residues: 7.6592 Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2170 Z= 0.214 Angle : 0.473 5.329 2979 Z= 0.266 Chirality : 0.039 0.112 368 Planarity : 0.003 0.028 357 Dihedral : 4.398 17.891 309 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.40 % Allowed : 20.87 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.50), residues: 277 helix: 2.80 (0.34), residues: 219 sheet: None (None), residues: 0 loop : -2.53 (0.61), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 282 TYR 0.008 0.001 TYR R 308 ARG 0.002 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.7761 (mtm180) cc_final: 0.5938 (mmt180) REVERT: R 84 LEU cc_start: 0.8218 (mm) cc_final: 0.7606 (mm) REVERT: R 151 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.6491 (mmt-90) REVERT: R 205 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7675 (mp) outliers start: 7 outliers final: 6 residues processed: 31 average time/residue: 0.2026 time to fit residues: 7.2968 Evaluate side-chains 34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2170 Z= 0.209 Angle : 0.471 5.326 2979 Z= 0.265 Chirality : 0.039 0.112 368 Planarity : 0.003 0.028 357 Dihedral : 4.376 17.895 309 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.40 % Allowed : 20.87 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.50), residues: 277 helix: 2.81 (0.34), residues: 219 sheet: None (None), residues: 0 loop : -2.57 (0.61), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.002 0.001 HIS R 178 PHE 0.009 0.001 PHE R 282 TYR 0.008 0.001 TYR R 308 ARG 0.002 0.000 ARG R 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.7767 (mtm180) cc_final: 0.5934 (mmt180) REVERT: R 84 LEU cc_start: 0.8216 (mm) cc_final: 0.7604 (mm) REVERT: R 151 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.6478 (mmt-90) REVERT: R 205 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7662 (mp) outliers start: 7 outliers final: 6 residues processed: 31 average time/residue: 0.1956 time to fit residues: 6.9613 Evaluate side-chains 34 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 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 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110051 restraints weight = 3104.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112400 restraints weight = 1688.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.114146 restraints weight = 1106.607| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2170 Z= 0.208 Angle : 0.470 5.333 2979 Z= 0.265 Chirality : 0.039 0.112 368 Planarity : 0.003 0.028 357 Dihedral : 4.368 17.885 309 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.40 % Allowed : 20.87 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.50), residues: 277 helix: 2.82 (0.34), residues: 219 sheet: None (None), residues: 0 loop : -2.57 (0.61), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 282 TYR 0.008 0.001 TYR R 308 ARG 0.002 0.000 ARG R 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 945.29 seconds wall clock time: 17 minutes 36.83 seconds (1056.83 seconds total)