Starting phenix.real_space_refine on Wed Mar 5 15:15:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfe_60058/03_2025/8zfe_60058.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfe_60058/03_2025/8zfe_60058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zfe_60058/03_2025/8zfe_60058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfe_60058/03_2025/8zfe_60058.map" model { file = "/net/cci-nas-00/data/ceres_data/8zfe_60058/03_2025/8zfe_60058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfe_60058/03_2025/8zfe_60058.cif" } resolution = 2.56 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= 0.017 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 12 5.16 5 C 1452 2.51 5 N 367 2.21 5 O 367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2198 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2198 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 280} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 134 Time building chain proxies: 2.21, per 1000 atoms: 1.01 Number of scatterers: 2198 At special positions: 0 Unit cell: (59.52, 63.24, 71.61, 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 12 16.00 O 367 8.00 N 367 7.00 C 1452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.54 Conformation dependent library (CDL) restraints added in 284.5 milliseconds 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 562 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 1 sheets defined 72.0% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'R' and resid 24 through 50 Proline residue: R 35 - end of helix removed outlier: 3.737A pdb=" N CYS R 38 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU R 39 " --> pdb=" O PRO R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 65 removed outlier: 4.211A pdb=" N VAL R 56 " --> pdb=" O ASN R 52 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 70 No H-bonds generated for 'chain 'R' and resid 68 through 70' Processing helix chain 'R' and resid 71 through 81 removed outlier: 3.734A pdb=" N TRP R 75 " --> pdb=" O THR R 71 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 122 removed outlier: 3.591A pdb=" N ILE R 107 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA R 108 " --> pdb=" O TYR R 104 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 120 " --> pdb=" O ASP R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 131 Processing helix chain 'R' and resid 132 through 151 removed outlier: 3.503A pdb=" N ASN R 151 " --> pdb=" O GLU R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 157 removed outlier: 3.898A pdb=" N PHE R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 192 removed outlier: 3.641A pdb=" N ALA R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP R 182 " --> pdb=" O ARG R 178 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE R 192 " --> pdb=" O VAL R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 211 Processing helix chain 'R' and resid 219 through 253 removed outlier: 3.676A pdb=" N SER R 230 " --> pdb=" O ARG R 226 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL R 235 " --> pdb=" O LEU R 231 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU R 236 " --> pdb=" O ILE R 232 " (cutoff:3.500A) Proline residue: R 241 - end of helix Processing helix chain 'R' and resid 266 through 277 Processing helix chain 'R' and resid 279 through 290 Proline residue: R 285 - end of helix removed outlier: 3.859A pdb=" N LEU R 290 " --> pdb=" O ILE R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 301 Processing sheet with id=AA1, first strand: chain 'R' and resid 161 through 162 removed outlier: 3.627A pdb=" N PHE R 161 " --> pdb=" O PHE R 169 " (cutoff:3.500A) 131 hydrogen bonds defined for protein. 390 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: 0.54 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: 1.17 - 1.30: 329 1.30 - 1.42: 664 1.42 - 1.55: 1253 1.55 - 1.68: 0 1.68 - 1.81: 16 Bond restraints: 2262 Sorted by residual: bond pdb=" C SER R 152 " pdb=" N ALA R 153 " ideal model delta sigma weight residual 1.331 1.529 -0.198 2.07e-02 2.33e+03 9.15e+01 bond pdb=" C HIS R 157 " pdb=" N ASP R 158 " ideal model delta sigma weight residual 1.330 1.414 -0.084 1.32e-02 5.74e+03 4.03e+01 bond pdb=" CA TYR R 165 " pdb=" C TYR R 165 " ideal model delta sigma weight residual 1.526 1.452 0.074 1.23e-02 6.61e+03 3.59e+01 bond pdb=" C TYR R 165 " pdb=" O TYR R 165 " ideal model delta sigma weight residual 1.232 1.169 0.063 1.36e-02 5.41e+03 2.16e+01 bond pdb=" C HIS R 167 " pdb=" O HIS R 167 " ideal model delta sigma weight residual 1.234 1.181 0.053 1.18e-02 7.18e+03 2.00e+01 ... (remaining 2257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 3009 1.91 - 3.82: 73 3.82 - 5.73: 16 5.73 - 7.64: 3 7.64 - 9.55: 1 Bond angle restraints: 3102 Sorted by residual: angle pdb=" N ASN R 166 " pdb=" CA ASN R 166 " pdb=" C ASN R 166 " ideal model delta sigma weight residual 113.38 120.93 -7.55 1.17e+00 7.31e-01 4.16e+01 angle pdb=" C ARG R 164 " pdb=" N TYR R 165 " pdb=" CA TYR R 165 " ideal model delta sigma weight residual 123.17 116.47 6.70 1.49e+00 4.50e-01 2.02e+01 angle pdb=" O PHE R 156 " pdb=" C PHE R 156 " pdb=" N HIS R 157 " ideal model delta sigma weight residual 122.03 126.32 -4.29 1.04e+00 9.25e-01 1.70e+01 angle pdb=" CA PHE R 156 " pdb=" C PHE R 156 " pdb=" N HIS R 157 " ideal model delta sigma weight residual 116.92 113.24 3.68 1.16e+00 7.43e-01 1.01e+01 angle pdb=" C HIS R 167 " pdb=" CA HIS R 167 " pdb=" CB HIS R 167 " ideal model delta sigma weight residual 109.38 115.74 -6.36 2.03e+00 2.43e-01 9.83e+00 ... (remaining 3097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.71: 1121 11.71 - 23.42: 117 23.42 - 35.13: 44 35.13 - 46.85: 7 46.85 - 58.56: 4 Dihedral angle restraints: 1293 sinusoidal: 425 harmonic: 868 Sorted by residual: dihedral pdb=" CA THR R 216 " pdb=" C THR R 216 " pdb=" N GLU R 217 " pdb=" CA GLU R 217 " ideal model delta harmonic sigma weight residual 180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PRO R 22 " pdb=" C PRO R 22 " pdb=" N PRO R 23 " pdb=" CA PRO R 23 " ideal model delta harmonic sigma weight residual 180.00 156.82 23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA GLY R 96 " pdb=" C GLY R 96 " pdb=" N PHE R 97 " pdb=" CA PHE R 97 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 1290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 354 0.106 - 0.213: 7 0.213 - 0.319: 1 0.319 - 0.426: 0 0.426 - 0.532: 2 Chirality restraints: 364 Sorted by residual: chirality pdb=" CA ASN R 166 " pdb=" N ASN R 166 " pdb=" C ASN R 166 " pdb=" CB ASN R 166 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.08e+00 chirality pdb=" CA HIS R 167 " pdb=" N HIS R 167 " pdb=" C HIS R 167 " pdb=" CB HIS R 167 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CA TYR R 165 " pdb=" N TYR R 165 " pdb=" C TYR R 165 " pdb=" CB TYR R 165 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 361 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 153 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C ALA R 153 " -0.052 2.00e-02 2.50e+03 pdb=" O ALA R 153 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO R 154 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 153 " -0.042 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO R 154 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO R 154 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 154 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 164 " 0.009 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C ARG R 164 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG R 164 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR R 165 " 0.012 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 633 2.80 - 3.33: 2193 3.33 - 3.85: 3690 3.85 - 4.38: 4116 4.38 - 4.90: 7028 Nonbonded interactions: 17660 Sorted by model distance: nonbonded pdb=" O VAL R 32 " pdb=" OG1 THR R 36 " model vdw 2.278 3.040 nonbonded pdb=" NH2 ARG R 249 " pdb=" OE1 GLU R 263 " model vdw 2.345 3.120 nonbonded pdb=" NE ARG R 249 " pdb=" OE2 GLU R 263 " model vdw 2.430 3.120 nonbonded pdb=" N ASP R 83 " pdb=" OD1 ASP R 83 " model vdw 2.439 3.120 nonbonded pdb=" O SER R 278 " pdb=" OG SER R 278 " model vdw 2.472 3.040 ... (remaining 17655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.020 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 : 0.008 0.198 2262 Z= 0.538 Angle : 0.764 9.546 3102 Z= 0.439 Chirality : 0.061 0.532 364 Planarity : 0.006 0.063 384 Dihedral : 12.272 58.557 731 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.48 % Allowed : 0.95 % Favored : 98.57 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 8.33 % 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: -2.16 (0.47), residues: 291 helix: -0.56 (0.36), residues: 200 sheet: None (None), residues: 0 loop : -3.35 (0.52), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 85 HIS 0.015 0.002 HIS R 167 PHE 0.009 0.001 PHE R 267 TYR 0.010 0.002 TYR R 104 ARG 0.004 0.001 ARG R 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.240 Fit side-chains REVERT: R 292 ASN cc_start: 0.8133 (p0) cc_final: 0.7916 (p0) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.7894 time to fit residues: 30.2536 Evaluate side-chains 31 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.0670 chunk 21 optimal weight: 0.4980 chunk 12 optimal weight: 0.3980 chunk 7 optimal weight: 0.0670 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 157 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.116357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107561 restraints weight = 3370.511| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.66 r_work: 0.3516 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2262 Z= 0.186 Angle : 0.605 7.477 3102 Z= 0.312 Chirality : 0.042 0.132 364 Planarity : 0.004 0.042 384 Dihedral : 5.193 21.124 317 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.90 % Allowed : 11.90 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.37 (0.49), residues: 291 helix: 0.04 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -3.39 (0.56), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 144 HIS 0.010 0.002 HIS R 167 PHE 0.007 0.001 PHE R 267 TYR 0.024 0.002 TYR R 270 ARG 0.004 0.001 ARG R 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.256 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 31 average time/residue: 1.1502 time to fit residues: 36.7932 Evaluate side-chains 28 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 25 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 18 optimal weight: 0.0470 chunk 4 optimal weight: 0.2980 chunk 22 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 26 optimal weight: 0.2980 overall best weight: 0.1836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.116033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.107023 restraints weight = 3353.884| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.62 r_work: 0.3520 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2262 Z= 0.163 Angle : 0.565 6.727 3102 Z= 0.290 Chirality : 0.041 0.127 364 Planarity : 0.004 0.031 384 Dihedral : 4.750 19.937 317 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.86 % Allowed : 12.86 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.01 (0.50), residues: 291 helix: 0.31 (0.37), residues: 209 sheet: None (None), residues: 0 loop : -3.26 (0.57), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 75 HIS 0.002 0.001 HIS R 123 PHE 0.006 0.001 PHE R 109 TYR 0.025 0.001 TYR R 270 ARG 0.008 0.001 ARG R 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 582 Ramachandran restraints generated. 291 Oldfield, 0 Emsley, 291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.238 Fit side-chains REVERT: R 176 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.4956 (ppp) outliers start: 6 outliers final: 4 residues processed: 28 average time/residue: 1.1043 time to fit residues: 31.8358 Evaluate side-chains 25 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 168 THR Chi-restraints excluded: chain R residue 176 MET Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4986 > 50: distance: 6 - 9: 35.570 distance: 9 - 10: 67.897 distance: 10 - 11: 40.301 distance: 10 - 13: 39.819 distance: 11 - 12: 56.635 distance: 11 - 14: 41.606 distance: 14 - 15: 40.922 distance: 15 - 16: 29.026 distance: 15 - 18: 40.538 distance: 16 - 17: 46.910 distance: 16 - 20: 41.033 distance: 18 - 19: 40.047 distance: 20 - 21: 57.238 distance: 21 - 22: 40.071 distance: 21 - 24: 40.884 distance: 22 - 23: 56.726 distance: 22 - 27: 56.310 distance: 27 - 28: 37.627 distance: 28 - 29: 55.889 distance: 28 - 31: 40.036 distance: 29 - 30: 57.599 distance: 29 - 33: 21.060 distance: 31 - 32: 40.954 distance: 33 - 34: 43.185 distance: 34 - 35: 56.814 distance: 35 - 36: 40.064 distance: 35 - 40: 39.659 distance: 37 - 38: 39.675 distance: 37 - 39: 58.047 distance: 41 - 44: 39.569 distance: 42 - 43: 55.738 distance: 45 - 46: 56.915 distance: 46 - 47: 39.579 distance: 46 - 49: 6.751 distance: 47 - 48: 40.252 distance: 47 - 50: 40.591 distance: 50 - 51: 40.362 distance: 51 - 52: 24.202 distance: 51 - 54: 55.518 distance: 52 - 53: 58.387 distance: 52 - 59: 15.375 distance: 53 - 82: 35.344 distance: 54 - 55: 41.489 distance: 55 - 56: 40.961 distance: 56 - 57: 12.691 distance: 56 - 58: 27.529 distance: 59 - 60: 53.008 distance: 60 - 61: 39.415 distance: 60 - 63: 6.672 distance: 61 - 62: 55.860 distance: 61 - 68: 56.169 distance: 62 - 90: 37.222 distance: 63 - 64: 57.402 distance: 65 - 66: 39.914 distance: 65 - 67: 42.571 distance: 69 - 70: 39.793 distance: 69 - 72: 56.091 distance: 70 - 71: 56.150 distance: 70 - 77: 34.579 distance: 71 - 98: 35.869 distance: 72 - 73: 17.323 distance: 73 - 74: 23.239 distance: 74 - 75: 57.124 distance: 75 - 76: 40.769