Starting phenix.real_space_refine on Sat Apr 4 22:31:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w02_65489/04_2026/9w02_65489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w02_65489/04_2026/9w02_65489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w02_65489/04_2026/9w02_65489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w02_65489/04_2026/9w02_65489.map" model { file = "/net/cci-nas-00/data/ceres_data/9w02_65489/04_2026/9w02_65489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w02_65489/04_2026/9w02_65489_neut.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.020 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: 5 Type Number sf(0) Gaussians P 49 5.49 5 S 24 5.16 5 C 2888 2.51 5 N 909 2.21 5 O 1030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4900 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1898 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 8, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1961 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} Chain: "C" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 774 Classifications: {'DNA': 1, 'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 14, 'rna3p': 22} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 1.32, per 1000 atoms: 0.27 Number of scatterers: 4900 At special positions: 0 Unit cell: (63.8, 65.975, 105.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 49 15.00 O 1030 8.00 N 909 7.00 C 2888 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: 0.56 Conformation dependent library (CDL) restraints added in 255.8 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 902 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 2 sheets defined 71.6% alpha, 3.3% beta 6 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 65 through 97 removed outlier: 3.659A pdb=" N LYS A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 92 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 134 removed outlier: 4.296A pdb=" N GLU A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.708A pdb=" N VAL A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.912A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.510A pdb=" N ARG A 185 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.528A pdb=" N TYR A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'B' and resid 66 through 98 removed outlier: 3.500A pdb=" N GLN B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 133 removed outlier: 3.570A pdb=" N LYS B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.598A pdb=" N GLN B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.818A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 removed outlier: 4.187A pdb=" N TYR B 186 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.609A pdb=" N LYS B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 231 Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 288 through 293 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 238 Processing sheet with id=AA2, first strand: chain 'B' and resid 234 through 238 253 hydrogen bonds defined for protein. 747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 926 1.32 - 1.45: 1475 1.45 - 1.57: 2561 1.57 - 1.70: 97 1.70 - 1.82: 44 Bond restraints: 5103 Sorted by residual: bond pdb=" C SER A 237 " pdb=" N ARG A 238 " ideal model delta sigma weight residual 1.330 1.236 0.094 1.39e-02 5.18e+03 4.53e+01 bond pdb=" C ARG A 238 " pdb=" N ASN A 239 " ideal model delta sigma weight residual 1.330 1.247 0.083 1.38e-02 5.25e+03 3.60e+01 bond pdb=" C SER A 105 " pdb=" N THR A 106 " ideal model delta sigma weight residual 1.335 1.267 0.068 1.31e-02 5.83e+03 2.70e+01 bond pdb=" C ALA A 206 " pdb=" N ASN A 207 " ideal model delta sigma weight residual 1.335 1.265 0.070 1.38e-02 5.25e+03 2.57e+01 bond pdb=" CA ASN B 195 " pdb=" C ASN B 195 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.32e-02 5.74e+03 9.34e+00 ... (remaining 5098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 5836 2.00 - 4.00: 1142 4.00 - 6.01: 130 6.01 - 8.01: 10 8.01 - 10.01: 1 Bond angle restraints: 7119 Sorted by residual: angle pdb=" N THR B 197 " pdb=" CA THR B 197 " pdb=" C THR B 197 " ideal model delta sigma weight residual 110.97 105.60 5.37 1.09e+00 8.42e-01 2.43e+01 angle pdb=" N ASN A 195 " pdb=" CA ASN A 195 " pdb=" C ASN A 195 " ideal model delta sigma weight residual 111.33 105.45 5.88 1.21e+00 6.83e-01 2.36e+01 angle pdb=" CB HIS B 296 " pdb=" CG HIS B 296 " pdb=" CD2 HIS B 296 " ideal model delta sigma weight residual 131.20 124.90 6.30 1.30e+00 5.92e-01 2.35e+01 angle pdb=" N VAL B 161 " pdb=" CA VAL B 161 " pdb=" C VAL B 161 " ideal model delta sigma weight residual 109.63 116.51 -6.88 1.44e+00 4.82e-01 2.28e+01 angle pdb=" CB HIS B 258 " pdb=" CG HIS B 258 " pdb=" CD2 HIS B 258 " ideal model delta sigma weight residual 131.20 125.21 5.99 1.30e+00 5.92e-01 2.12e+01 ... (remaining 7114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 2895 34.36 - 68.71: 162 68.71 - 103.07: 16 103.07 - 137.42: 0 137.42 - 171.78: 3 Dihedral angle restraints: 3076 sinusoidal: 1679 harmonic: 1397 Sorted by residual: dihedral pdb=" O4' C C 24 " pdb=" C1' C C 24 " pdb=" N1 C C 24 " pdb=" C2 C C 24 " ideal model delta sinusoidal sigma weight residual 200.00 36.54 163.46 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" C5' A C 29 " pdb=" C4' A C 29 " pdb=" C3' A C 29 " pdb=" O3' A C 29 " ideal model delta sinusoidal sigma weight residual 82.00 128.05 -46.05 1 8.00e+00 1.56e-02 4.59e+01 dihedral pdb=" O4' A C 29 " pdb=" C4' A C 29 " pdb=" C3' A C 29 " pdb=" C2' A C 29 " ideal model delta sinusoidal sigma weight residual -35.00 10.27 -45.27 1 8.00e+00 1.56e-02 4.44e+01 ... (remaining 3073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 640 0.104 - 0.207: 147 0.207 - 0.311: 10 0.311 - 0.415: 1 0.415 - 0.518: 2 Chirality restraints: 800 Sorted by residual: chirality pdb=" P G C 36 " pdb=" OP1 G C 36 " pdb=" OP2 G C 36 " pdb=" O5' G C 36 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" P A C 37 " pdb=" OP1 A C 37 " pdb=" OP2 A C 37 " pdb=" O5' A C 37 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.14e+00 chirality pdb=" CA TYR A 160 " pdb=" N TYR A 160 " pdb=" C TYR A 160 " pdb=" CB TYR A 160 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 797 not shown) Planarity restraints: 731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 309 " 0.131 2.00e-02 2.50e+03 6.75e-02 1.14e+02 pdb=" CG TRP B 309 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 309 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 309 " -0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP B 309 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP B 309 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP B 309 " -0.081 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 309 " 0.080 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 309 " -0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP B 309 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 175 " 0.095 2.00e-02 2.50e+03 5.47e-02 5.99e+01 pdb=" CG TYR A 175 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 175 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 175 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR A 175 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR A 175 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR A 175 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 175 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 173 " -0.080 2.00e-02 2.50e+03 4.43e-02 4.91e+01 pdb=" CG TRP B 173 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP B 173 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 173 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP B 173 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP B 173 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP B 173 " 0.071 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 173 " -0.037 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 173 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 173 " -0.059 2.00e-02 2.50e+03 ... (remaining 728 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1832 2.91 - 3.41: 5083 3.41 - 3.90: 9146 3.90 - 4.40: 10192 4.40 - 4.90: 15553 Nonbonded interactions: 41806 Sorted by model distance: nonbonded pdb=" OH TYR A 95 " pdb=" O ARG A 103 " model vdw 2.411 3.040 nonbonded pdb=" O4' C C 24 " pdb=" O2 C C 24 " model vdw 2.436 3.040 nonbonded pdb=" O2' C C 8 " pdb=" OP2 C C 9 " model vdw 2.458 3.040 nonbonded pdb=" O GLY A 194 " pdb=" C ASN A 195 " model vdw 2.461 3.270 nonbonded pdb=" N LYS B 133 " pdb=" O LYS B 133 " model vdw 2.474 2.496 ... (remaining 41801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 65 through 289 or resid 298 through 309)) } 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: 3.390 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.890 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 : 0.011 0.094 5103 Z= 0.697 Angle : 1.531 10.010 7119 Z= 1.046 Chirality : 0.084 0.518 800 Planarity : 0.013 0.093 731 Dihedral : 19.612 171.778 2174 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.50 % Allowed : 5.21 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.34), residues: 476 helix: 0.06 (0.25), residues: 314 sheet: None (None), residues: 0 loop : 0.40 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 263 TYR 0.095 0.014 TYR A 175 PHE 0.035 0.009 PHE B 109 TRP 0.131 0.016 TRP B 309 HIS 0.011 0.003 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.01081 ( 5103) covalent geometry : angle 1.53085 ( 7119) hydrogen bonds : bond 0.18771 ( 268) hydrogen bonds : angle 6.77596 ( 773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9231 (tpp) cc_final: 0.9025 (tpp) REVERT: A 86 MET cc_start: 0.8592 (ttp) cc_final: 0.8243 (tmm) REVERT: A 90 ASN cc_start: 0.8283 (m-40) cc_final: 0.8022 (m110) REVERT: A 105 SER cc_start: 0.9221 (m) cc_final: 0.8932 (t) REVERT: A 164 GLU cc_start: 0.8777 (tp30) cc_final: 0.8554 (tp30) REVERT: A 288 LEU cc_start: 0.8799 (mm) cc_final: 0.8541 (tp) REVERT: A 289 TYR cc_start: 0.8699 (m-80) cc_final: 0.8191 (m-10) outliers start: 2 outliers final: 3 residues processed: 70 average time/residue: 0.4742 time to fit residues: 34.8058 Evaluate side-chains 47 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 131 HIS B 134 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.085051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.069415 restraints weight = 13314.442| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.02 r_work: 0.3137 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5103 Z= 0.163 Angle : 0.613 8.348 7119 Z= 0.339 Chirality : 0.039 0.199 800 Planarity : 0.004 0.027 731 Dihedral : 22.448 174.137 1214 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.24 % Allowed : 11.17 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.37), residues: 476 helix: 2.53 (0.28), residues: 321 sheet: None (None), residues: 0 loop : 1.08 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 238 TYR 0.023 0.002 TYR A 95 PHE 0.012 0.002 PHE A 269 TRP 0.009 0.001 TRP B 309 HIS 0.004 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5103) covalent geometry : angle 0.61282 ( 7119) hydrogen bonds : bond 0.06225 ( 268) hydrogen bonds : angle 3.86925 ( 773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.175 Fit side-chains REVERT: A 86 MET cc_start: 0.8577 (ttp) cc_final: 0.8159 (tmm) REVERT: A 90 ASN cc_start: 0.8459 (m-40) cc_final: 0.8169 (m110) REVERT: A 105 SER cc_start: 0.9077 (m) cc_final: 0.8607 (t) REVERT: A 164 GLU cc_start: 0.8856 (tp30) cc_final: 0.8618 (tp30) REVERT: A 288 LEU cc_start: 0.8913 (mm) cc_final: 0.8707 (tp) REVERT: B 205 MET cc_start: 0.8427 (tpt) cc_final: 0.8194 (tpt) REVERT: B 274 TRP cc_start: 0.8489 (t60) cc_final: 0.8092 (t60) outliers start: 5 outliers final: 2 residues processed: 59 average time/residue: 0.4263 time to fit residues: 26.4393 Evaluate side-chains 46 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 146 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.083261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.067848 restraints weight = 13296.151| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.97 r_work: 0.3106 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5103 Z= 0.171 Angle : 0.584 7.678 7119 Z= 0.315 Chirality : 0.038 0.174 800 Planarity : 0.004 0.035 731 Dihedral : 22.128 171.086 1211 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.49 % Allowed : 15.38 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.65 (0.37), residues: 476 helix: 3.01 (0.27), residues: 320 sheet: None (None), residues: 0 loop : 1.26 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 218 TYR 0.022 0.002 TYR A 95 PHE 0.009 0.001 PHE A 269 TRP 0.008 0.001 TRP B 309 HIS 0.003 0.001 HIS B 258 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5103) covalent geometry : angle 0.58442 ( 7119) hydrogen bonds : bond 0.05399 ( 268) hydrogen bonds : angle 3.62941 ( 773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.7360 (mtt) cc_final: 0.7065 (mtm) REVERT: A 105 SER cc_start: 0.8999 (m) cc_final: 0.8497 (t) REVERT: A 164 GLU cc_start: 0.8853 (tp30) cc_final: 0.8604 (tp30) REVERT: B 205 MET cc_start: 0.8554 (tpt) cc_final: 0.8224 (tpp) REVERT: B 274 TRP cc_start: 0.8537 (t60) cc_final: 0.8176 (t60) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.4764 time to fit residues: 26.4818 Evaluate side-chains 48 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 178 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6696 > 50: distance: 50 - 55: 12.741 distance: 55 - 56: 9.201 distance: 56 - 57: 13.606 distance: 56 - 59: 13.318 distance: 57 - 58: 9.516 distance: 57 - 63: 11.848 distance: 59 - 60: 33.201 distance: 60 - 61: 30.327 distance: 60 - 62: 8.848 distance: 63 - 64: 30.751 distance: 64 - 65: 25.203 distance: 64 - 67: 19.805 distance: 65 - 66: 21.089 distance: 65 - 70: 5.372 distance: 67 - 68: 15.969 distance: 67 - 69: 24.436 distance: 70 - 71: 31.802 distance: 71 - 72: 43.602 distance: 71 - 74: 29.200 distance: 72 - 73: 31.488 distance: 72 - 81: 11.703 distance: 74 - 75: 7.930 distance: 75 - 76: 9.773 distance: 76 - 77: 30.339 distance: 77 - 78: 11.113 distance: 78 - 79: 40.237 distance: 78 - 80: 23.340 distance: 81 - 82: 9.965 distance: 81 - 87: 69.670 distance: 82 - 83: 32.443 distance: 82 - 85: 38.772 distance: 83 - 84: 51.530 distance: 83 - 88: 8.132 distance: 85 - 86: 38.884 distance: 89 - 90: 22.331 distance: 89 - 92: 41.521 distance: 90 - 91: 19.640 distance: 90 - 96: 8.480 distance: 92 - 93: 3.755 distance: 93 - 94: 28.642 distance: 93 - 95: 33.513 distance: 96 - 97: 37.282 distance: 97 - 98: 28.130 distance: 97 - 100: 17.772 distance: 98 - 99: 8.592 distance: 100 - 101: 9.687 distance: 101 - 102: 12.905 distance: 101 - 103: 4.451 distance: 102 - 104: 8.034 distance: 103 - 105: 13.120 distance: 105 - 106: 8.831 distance: 106 - 107: 7.164 distance: 108 - 109: 21.580 distance: 109 - 110: 18.158 distance: 110 - 112: 56.436 distance: 112 - 113: 12.593 distance: 113 - 114: 46.808 distance: 113 - 116: 34.233 distance: 114 - 115: 41.641 distance: 114 - 120: 13.827 distance: 116 - 117: 5.432 distance: 116 - 118: 39.976 distance: 117 - 119: 7.983 distance: 120 - 121: 28.727 distance: 121 - 122: 13.641 distance: 121 - 124: 5.320 distance: 122 - 123: 37.704 distance: 122 - 127: 14.088 distance: 124 - 126: 14.734 distance: 127 - 128: 35.056 distance: 128 - 129: 24.181 distance: 128 - 131: 21.453 distance: 129 - 130: 12.276 distance: 129 - 136: 20.956 distance: 130 - 158: 21.504 distance: 131 - 132: 15.026 distance: 132 - 133: 45.605 distance: 133 - 134: 4.074 distance: 133 - 135: 13.671