Starting phenix.real_space_refine on Fri Apr 5 12:24:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggt_40020/04_2024/8ggt_40020_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggt_40020/04_2024/8ggt_40020.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/8ggt_40020/04_2024/8ggt_40020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggt_40020/04_2024/8ggt_40020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggt_40020/04_2024/8ggt_40020_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggt_40020/04_2024/8ggt_40020_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= 0.023 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 1405 2.51 5 N 335 2.21 5 O 350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2105 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2090 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 95 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: 1.89, per 1000 atoms: 0.90 Number of scatterers: 2105 At special positions: 0 Unit cell: (56.4005, 84.1669, 61.6067, 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 350 8.00 N 335 7.00 C 1405 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 - 3.50 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: 0.95 Conformation dependent library (CDL) restraints added in 393.6 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... running ksdssp... Secondary structure from input PDB file: 11 helices and 0 sheets defined 80.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'R' and resid 38 through 60 removed outlier: 3.787A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 95 removed outlier: 4.412A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 5.254A 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 103 through 136 Processing helix chain 'R' and resid 139 through 144 removed outlier: 4.208A pdb=" N GLN R 142 " --> pdb=" O PHE R 139 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER R 143 " --> pdb=" O LYS R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 171 removed outlier: 4.062A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 4.132A 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 179 through 186 Processing helix chain 'R' and resid 197 through 207 Processing helix chain 'R' and resid 209 through 236 removed outlier: 3.835A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 298 removed outlier: 3.842A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.674A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 326 removed outlier: 3.763A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 339 147 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: 0.53 Time building geometry restraints manager: 1.04 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: 385 1.33 - 1.45: 561 1.45 - 1.57: 1190 1.57 - 1.69: 1 1.69 - 1.81: 22 Bond restraints: 2159 Sorted by residual: bond pdb=" C LEU R 287 " pdb=" O LEU R 287 " ideal model delta sigma weight residual 1.244 1.211 0.032 9.80e-03 1.04e+04 1.09e+01 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 7.10e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.576 -0.053 2.00e-02 2.50e+03 6.91e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.567 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.440 -0.046 2.00e-02 2.50e+03 5.28e+00 ... (remaining 2154 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.42: 58 107.42 - 114.08: 1249 114.08 - 120.74: 1025 120.74 - 127.40: 606 127.40 - 134.06: 23 Bond angle restraints: 2961 Sorted by residual: angle pdb=" N PHE R 289 " pdb=" CA PHE R 289 " pdb=" C PHE R 289 " ideal model delta sigma weight residual 111.07 118.45 -7.38 1.07e+00 8.73e-01 4.75e+01 angle pdb=" N TRP R 286 " pdb=" CA TRP R 286 " pdb=" C TRP R 286 " ideal model delta sigma weight residual 113.97 121.51 -7.54 1.28e+00 6.10e-01 3.47e+01 angle pdb=" CA MET R 36 " pdb=" CB MET R 36 " pdb=" CG MET R 36 " ideal model delta sigma weight residual 114.10 121.69 -7.59 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CB MET R 36 " pdb=" CG MET R 36 " pdb=" SD MET R 36 " ideal model delta sigma weight residual 112.70 123.66 -10.96 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C LEU R 287 " pdb=" N PRO R 288 " pdb=" CA PRO R 288 " ideal model delta sigma weight residual 119.05 115.01 4.04 1.11e+00 8.12e-01 1.32e+01 ... (remaining 2956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 1124 16.67 - 33.33: 81 33.33 - 49.99: 25 49.99 - 66.66: 2 66.66 - 83.32: 3 Dihedral angle restraints: 1235 sinusoidal: 407 harmonic: 828 Sorted by residual: dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual -86.00 -169.32 83.32 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CA LEU R 302 " pdb=" C LEU R 302 " pdb=" N ILE R 303 " pdb=" CA ILE R 303 " ideal model delta harmonic sigma weight residual 180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+01 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 -161.81 -18.19 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 1232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 254 0.042 - 0.083: 90 0.083 - 0.124: 18 0.124 - 0.165: 0 0.165 - 0.207: 2 Chirality restraints: 364 Sorted by residual: chirality pdb=" CA TRP R 286 " pdb=" N TRP R 286 " pdb=" C TRP R 286 " pdb=" CB TRP R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 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 2.57 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA PHE R 289 " pdb=" N PHE R 289 " pdb=" C PHE R 289 " pdb=" CB PHE R 289 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 361 not shown) Planarity restraints: 358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 36 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C MET R 36 " 0.035 2.00e-02 2.50e+03 pdb=" O MET R 36 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY R 37 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 287 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO R 288 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 288 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 288 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 281 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C THR R 281 " 0.026 2.00e-02 2.50e+03 pdb=" O THR R 281 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE R 282 " -0.009 2.00e-02 2.50e+03 ... (remaining 355 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 408 2.77 - 3.30: 2088 3.30 - 3.84: 3352 3.84 - 4.37: 3374 4.37 - 4.90: 6290 Nonbonded interactions: 15512 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.240 2.440 nonbonded pdb=" OD2 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.307 2.440 nonbonded pdb=" NE1 TRP R 99 " pdb=" O GLY R 102 " model vdw 2.504 2.520 nonbonded pdb=" OH TYR R 185 " pdb=" O PHE R 194 " model vdw 2.527 2.440 nonbonded pdb=" OG SER R 165 " pdb=" N PHE R 166 " model vdw 2.531 2.520 ... (remaining 15507 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.050 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.850 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 0.053 2159 Z= 0.297 Angle : 0.700 10.965 2961 Z= 0.420 Chirality : 0.041 0.207 364 Planarity : 0.004 0.039 358 Dihedral : 13.407 78.387 694 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.49), residues: 277 helix: 2.41 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -2.50 (0.55), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 313 HIS 0.002 0.001 HIS R 178 PHE 0.012 0.001 PHE R 139 TYR 0.009 0.001 TYR R 199 ARG 0.001 0.000 ARG R 151 *********************** 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 21 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.174 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1420 time to fit residues: 3.6544 Evaluate side-chains 16 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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: 0.5980 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2159 Z= 0.245 Angle : 0.532 6.281 2961 Z= 0.297 Chirality : 0.041 0.146 364 Planarity : 0.004 0.034 358 Dihedral : 4.682 17.918 311 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.50 % Allowed : 6.00 % Favored : 92.50 % 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: 2.11 (0.50), residues: 277 helix: 2.50 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -2.40 (0.63), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 286 HIS 0.003 0.001 HIS R 296 PHE 0.015 0.001 PHE R 139 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 *********************** 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 23 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.240 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.1732 time to fit residues: 4.5768 Evaluate side-chains 21 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 309 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2159 Z= 0.223 Angle : 0.508 6.274 2961 Z= 0.282 Chirality : 0.040 0.134 364 Planarity : 0.004 0.029 358 Dihedral : 4.583 18.041 311 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.50 % Allowed : 9.00 % Favored : 89.50 % 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: 2.31 (0.51), residues: 277 helix: 2.73 (0.36), residues: 201 sheet: None (None), residues: 0 loop : -2.00 (0.63), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 286 HIS 0.003 0.001 HIS R 296 PHE 0.014 0.001 PHE R 139 TYR 0.010 0.001 TYR R 308 ARG 0.001 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 22 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.236 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 21 average time/residue: 0.1450 time to fit residues: 3.7098 Evaluate side-chains 21 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 218 VAL 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: 0.9980 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.0000 chunk 24 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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: 0.7833 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2159 Z= 0.199 Angle : 0.492 7.318 2961 Z= 0.271 Chirality : 0.039 0.129 364 Planarity : 0.004 0.028 358 Dihedral : 4.467 17.463 311 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.50 % Allowed : 11.00 % Favored : 86.50 % 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: 2.30 (0.51), residues: 277 helix: 2.76 (0.35), residues: 202 sheet: None (None), residues: 0 loop : -2.21 (0.64), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 286 HIS 0.003 0.001 HIS R 296 PHE 0.011 0.001 PHE R 139 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 151 *********************** 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 27 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.239 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.1968 time to fit residues: 5.7330 Evaluate side-chains 22 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7827 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2159 Z= 0.191 Angle : 0.497 8.231 2961 Z= 0.270 Chirality : 0.039 0.126 364 Planarity : 0.004 0.028 358 Dihedral : 4.383 17.247 311 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.00 % Allowed : 14.50 % Favored : 83.50 % 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: 2.35 (0.52), residues: 277 helix: 2.78 (0.35), residues: 202 sheet: None (None), residues: 0 loop : -2.15 (0.66), residues: 75 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 0.010 0.001 PHE R 139 TYR 0.009 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 24 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.227 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 0.1276 time to fit residues: 3.5824 Evaluate side-chains 23 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2159 Z= 0.194 Angle : 0.504 9.206 2961 Z= 0.272 Chirality : 0.039 0.125 364 Planarity : 0.004 0.027 358 Dihedral : 4.359 17.133 311 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.50 % Allowed : 16.00 % Favored : 82.50 % 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: 2.41 (0.52), residues: 277 helix: 2.80 (0.35), residues: 202 sheet: None (None), residues: 0 loop : -2.03 (0.69), residues: 75 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 0.010 0.001 PHE R 139 TYR 0.008 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 *********************** 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 24 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: R 40 MET cc_start: 0.7435 (mtt) cc_final: 0.7134 (mtt) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.1810 time to fit residues: 4.9410 Evaluate side-chains 23 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 218 VAL 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: 0.4980 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7845 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2159 Z= 0.207 Angle : 0.516 9.764 2961 Z= 0.277 Chirality : 0.039 0.123 364 Planarity : 0.004 0.028 358 Dihedral : 4.396 17.044 311 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.50 % Allowed : 16.50 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.52), residues: 277 helix: 2.75 (0.35), residues: 202 sheet: None (None), residues: 0 loop : -1.93 (0.71), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE R 139 TYR 0.008 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 *********************** 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 23 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: R 40 MET cc_start: 0.7434 (mtt) cc_final: 0.7131 (mtt) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.1248 time to fit residues: 3.5128 Evaluate side-chains 23 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 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: 0.3980 chunk 23 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.0000 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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: 0.7812 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2159 Z= 0.172 Angle : 0.502 10.502 2961 Z= 0.267 Chirality : 0.038 0.121 364 Planarity : 0.004 0.028 358 Dihedral : 4.267 17.015 311 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.50 % Allowed : 16.50 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.52), residues: 277 helix: 2.85 (0.35), residues: 202 sheet: None (None), residues: 0 loop : -1.91 (0.72), residues: 75 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 0.007 0.001 PHE R 139 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 *********************** 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 23 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: R 40 MET cc_start: 0.7413 (mtt) cc_final: 0.7101 (mtt) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.1630 time to fit residues: 4.2689 Evaluate side-chains 22 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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: 0.7816 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2159 Z= 0.181 Angle : 0.504 10.844 2961 Z= 0.268 Chirality : 0.038 0.118 364 Planarity : 0.004 0.028 358 Dihedral : 4.253 16.795 311 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.50 % Allowed : 16.50 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.52), residues: 277 helix: 2.85 (0.35), residues: 202 sheet: None (None), residues: 0 loop : -1.92 (0.72), residues: 75 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 0.007 0.001 PHE R 139 TYR 0.008 0.001 TYR R 308 ARG 0.001 0.000 ARG R 151 *********************** 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 24 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: R 40 MET cc_start: 0.7411 (mtt) cc_final: 0.7097 (mtt) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.1613 time to fit residues: 4.5066 Evaluate side-chains 22 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.0541 > 50: distance: 12 - 79: 6.602 distance: 63 - 68: 4.052 distance: 69 - 70: 4.644 distance: 70 - 71: 10.466 distance: 70 - 74: 7.251 distance: 72 - 73: 4.622 distance: 75 - 76: 6.829 distance: 75 - 78: 4.772 distance: 76 - 77: 14.387 distance: 76 - 80: 15.528 distance: 78 - 79: 6.363 distance: 80 - 81: 26.227 distance: 81 - 82: 18.391 distance: 81 - 84: 16.142 distance: 82 - 83: 19.194 distance: 82 - 85: 24.905 distance: 85 - 86: 11.865 distance: 86 - 87: 10.420 distance: 86 - 89: 9.594 distance: 87 - 88: 12.510 distance: 87 - 96: 7.601 distance: 89 - 90: 11.304 distance: 90 - 91: 7.271 distance: 90 - 92: 5.352 distance: 92 - 94: 3.395 distance: 93 - 95: 6.344 distance: 94 - 95: 5.278 distance: 97 - 100: 12.648 distance: 98 - 99: 10.920 distance: 100 - 101: 7.050 distance: 101 - 102: 6.705 distance: 101 - 103: 3.781 distance: 102 - 104: 4.205 distance: 103 - 105: 4.646 distance: 104 - 106: 3.645 distance: 105 - 106: 6.988 distance: 107 - 108: 4.978 distance: 108 - 109: 7.066 distance: 108 - 111: 6.387 distance: 109 - 110: 20.330 distance: 109 - 112: 7.442 distance: 112 - 113: 8.214 distance: 113 - 114: 11.772 distance: 113 - 116: 14.327 distance: 114 - 115: 15.108 distance: 114 - 117: 4.127 distance: 118 - 121: 3.187 distance: 119 - 120: 3.498 distance: 119 - 126: 4.213 distance: 120 - 148: 7.229 distance: 121 - 122: 3.267 distance: 126 - 127: 4.005 distance: 127 - 128: 4.824 distance: 127 - 130: 10.490 distance: 129 - 156: 4.482 distance: 131 - 132: 4.439 distance: 132 - 133: 3.266 distance: 132 - 135: 5.671 distance: 133 - 134: 3.702 distance: 134 - 160: 3.782 distance: 135 - 136: 4.825 distance: 136 - 137: 6.197 distance: 136 - 138: 3.549 distance: 137 - 139: 5.460 distance: 139 - 141: 5.503 distance: 140 - 141: 5.114