Starting phenix.real_space_refine on Wed Nov 20 13:14:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7o_36044/11_2024/8j7o_36044_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7o_36044/11_2024/8j7o_36044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7o_36044/11_2024/8j7o_36044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7o_36044/11_2024/8j7o_36044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7o_36044/11_2024/8j7o_36044_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7o_36044/11_2024/8j7o_36044_neut_trim.cif" } resolution = 3.83 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= -0.002 sd= 0.035 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 148 5.16 5 C 13448 2.51 5 N 3632 2.21 5 O 3940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 169 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21168 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5277 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 641} Chain: "B" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5277 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 641} Chain: "C" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5277 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 641} Chain: "E" Number of atoms: 5277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5277 Classifications: {'pe------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5277 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 : 0.012 0.103 21648 Z= 0.794 Angle : 1.603 14.477 29348 Z= 1.081 Chirality : 0.087 0.463 3276 Planarity : 0.012 0.125 3848 Dihedral : 12.721 86.045 8132 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.61 % Favored : 98.32 % Rotamer: Outliers : 2.65 % Allowed : 3.53 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 2740 helix: 0.18 (0.13), residues: 1216 sheet: -0.50 (0.28), residues: 328 loop : -0.24 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP B 624 HIS 0.029 0.004 HIS B 771 PHE 0.053 0.010 PHE A 618 TYR 0.097 0.016 TYR E 593 ARG 0.018 0.001 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5480 Ramachandran restraints generated. 2740 Oldfield, 0 Emsley, 2740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 354 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 634 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6718 (mp) REVERT: E 606 ASN cc_start: 0.6635 (OUTLIER) cc_final: 0.6141 (p0) REVERT: E 783 MET cc_start: 0.7424 (mmp) cc_final: 0.7216 (mmp) REVERT: E 1166 MET cc_start: 0.2997 (ttt) cc_final: 0.2598 (mtp) outliers start: 60 outliers final: 12 residues processed: 400 average time/residue: 0.2957 time to fit residues: 170.4746 Evaluate side-chains 192 residues out of total 2264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 1036 ARG Chi-restraints excluded: chain C residue 571 ARG Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 1036 ARG Chi-restraints excluded: chain C residue 1096 LYS Chi-restraints excluded: chain E residue 571 ARG Chi-restraints excluded: chain E residue 606 ASN Chi-restraints excluded: chain E residue 836 GLU Chi-restraints excluded: chain E residue 1096 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 8.9990 chunk 206 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: