Starting phenix.real_space_refine on Wed Apr 17 16:56:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyr_26192/04_2024/7tyr_26192.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyr_26192/04_2024/7tyr_26192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyr_26192/04_2024/7tyr_26192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyr_26192/04_2024/7tyr_26192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyr_26192/04_2024/7tyr_26192.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyr_26192/04_2024/7tyr_26192.pdb" } resolution = 3.33 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= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13911 atoms to isotropic. 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 202 5.16 5 C 20214 2.51 5 N 5348 2.21 5 O 5846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A TYR 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 850": "OE1" <-> "OE2" Residue "A GLU 950": "OE1" <-> "OE2" Residue "A PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A ASP 1027": "OD1" <-> "OD2" Residue "A GLU 1097": "OE1" <-> "OE2" Residue "A ASP 1132": "OD1" <-> "OD2" Residue "A GLU 1139": "OE1" <-> "OE2" Residue "A ASP 1210": "OD1" <-> "OD2" Residue "A GLU 1557": "OE1" <-> "OE2" Residue "A GLU 1565": "OE1" <-> "OE2" Residue "A GLU 1570": "OE1" <-> "OE2" Residue "A PHE 1605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1728": "OE1" <-> "OE2" Residue "A PHE 1736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1751": "OE1" <-> "OE2" Residue "A GLU 1769": "OE1" <-> "OE2" Residue "A GLU 1799": "OE1" <-> "OE2" Residue "A GLU 1838": "OE1" <-> "OE2" Residue "A GLU 2087": "OE1" <-> "OE2" Residue "A GLU 2115": "OE1" <-> "OE2" Residue "A PHE 2309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2339": "OE1" <-> "OE2" Residue "A GLU 2430": "OE1" <-> "OE2" Residue "A GLU 2528": "OE1" <-> "OE2" Residue "A GLU 2578": "OE1" <-> "OE2" Residue "A GLU 2895": "OE1" <-> "OE2" Residue "A GLU 2974": "OE1" <-> "OE2" Residue "A ASP 2980": "OD1" <-> "OD2" Residue "A TYR 3114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3140": "OE1" <-> "OE2" Residue "A ASP 3180": "OD1" <-> "OD2" Residue "A GLU 3361": "OE1" <-> "OE2" Residue "A PHE 3382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3427": "OE1" <-> "OE2" Residue "A GLU 3478": "OE1" <-> "OE2" Residue "A ASP 3507": "OD1" <-> "OD2" Residue "A PHE 3585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3756": "OE1" <-> "OE2" Residue "A ASP 3778": "OD1" <-> "OD2" Residue "A GLU 3823": "OE1" <-> "OE2" Residue "A ASP 3851": "OD1" <-> "OD2" Residue "A GLU 3875": "OE1" <-> "OE2" Residue "A GLU 3933": "OE1" <-> "OE2" Residue "C ASP 384": "OD1" <-> "OD2" Residue "C GLU 409": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31610 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 31173 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3905, 31162 Classifications: {'peptide': 3905} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 179, 'TRANS': 3725} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 3905, 31162 Classifications: {'peptide': 3905} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 179, 'TRANS': 3725} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 31806 Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 437 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 8, 'TRANS': 43} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A4011 " occ=0.40 ... (20 atoms not shown) pdb=" CZ BPHE A4011 " occ=0.60 Time building chain proxies: 31.07, per 1000 atoms: 0.98 Number of scatterers: 31610 At special positions: 0 Unit cell: (128.52, 149.04, 185.76, 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 202 16.00 O 5846 8.00 N 5348 7.00 C 20214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1942 " - pdb=" SG CYS A2093 " distance=2.04 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 aSet 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: 6.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.040 Extract box with map and model: 29.040 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 112.700 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.220 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 32284 Z= 0.267 Angle : 0.758 10.580 43659 Z= 0.476 Chirality : 0.048 0.305 4903 Planarity : 0.005 0.077 5587 Dihedral : 19.611 89.881 12180 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.10 % Favored : 94.73 % Rotamer: Outliers : 2.70 % Allowed : 29.48 % Favored : 67.82 % 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: 0.19 (0.13), residues: 3948 helix: 1.24 (0.10), residues: 2507 sheet: 1.37 (0.76), residues: 43 loop : -2.04 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 300 HIS 0.009 0.001 HIS A1115 PHE 0.033 0.001 PHE A3382 TYR 0.015 0.001 TYR A3828 ARG 0.010 0.000 ARG A1712 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 599 time to evaluate : 2.629 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: A 8 VAL cc_start: 0.7662 (p) cc_final: 0.7372 (p) REVERT: A 134 LEU cc_start: 0.7964 (tt) cc_final: 0.7742 (tp) REVERT: A 541 MET cc_start: 0.8029 (tpp) cc_final: 0.7692 (mmm) REVERT: A 2224 PHE cc_start: 0.8197 (t80) cc_final: 0.7985 (t80) REVERT: A 2500 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7682 (mmtm) REVERT: A 3576 ASP cc_start: 0.8764 (t0) cc_final: 0.8309 (t0) outliers start: 95 outliers final: 20 residues processed: 660 average time/residue: 0.4584 time to fit residues: 463.2785 Evaluate side-chains 323 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 302 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 881 LYS Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1525 CYS Chi-restraints excluded: chain A residue 2094 MET Chi-restraints excluded: chain A residue 2126 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2500 LYS Chi-restraints excluded: chain A residue 2915 ARG Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 ARG Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 0.9980 chunk 299 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 159 optimal weight: 0.0970 chunk 309 optimal weight: 0.2980 chunk 119 optimal weight: 5.9990 chunk 188 optimal weight: 0.5980 chunk 230 optimal weight: 2.9990 chunk 358 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 613 HIS A 676 ASN A 857 GLN A1084 ASN A1466 ASN A1476 HIS ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2130 HIS ** A2177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2234 ASN A2352 HIS A2977 ASN ** A3059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3440 GLN ** A3671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3760 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32284 Z= 0.184 Angle : 0.626 14.504 43659 Z= 0.313 Chirality : 0.039 0.193 4903 Planarity : 0.005 0.093 5587 Dihedral : 5.317 70.565 4317 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.21 % Allowed : 28.60 % Favored : 69.18 % 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: 0.75 (0.14), residues: 3948 helix: 1.69 (0.11), residues: 2547 sheet: 0.99 (0.73), residues: 43 loop : -1.94 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2164 HIS 0.010 0.001 HIS A2352 PHE 0.029 0.001 PHE A2157 TYR 0.019 0.001 TYR C 391 ARG 0.010 0.000 ARG A2776 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 339 time to evaluate : 4.120 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: A 144 MET cc_start: 0.7127 (tpp) cc_final: 0.6479 (ttt) REVERT: A 208 MET cc_start: 0.6683 (ppp) cc_final: 0.5992 (mtt) REVERT: A 916 GLU cc_start: 0.7903 (tt0) cc_final: 0.7618 (tt0) REVERT: A 3218 MET cc_start: 0.2470 (OUTLIER) cc_final: 0.1296 (mmp) REVERT: A 3411 ASP cc_start: 0.8667 (t70) cc_final: 0.8332 (t0) REVERT: A 3576 ASP cc_start: 0.8829 (t0) cc_final: 0.8516 (t0) REVERT: A 4087 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7531 (m-70) outliers start: 78 outliers final: 30 residues processed: 395 average time/residue: 0.4489 time to fit residues: 288.7795 Evaluate side-chains 312 residues out of total 3527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 280 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1476 HIS Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1525 CYS Chi-restraints excluded: chain A residue 1607 GLU Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1814 PHE Chi-restraints excluded: chain A residue 1845 VAL Chi-restraints excluded: chain A residue 1914 THR Chi-restraints excluded: chain A residue 2027 SER Chi-restraints excluded: chain A residue 2041 SER Chi-restraints excluded: chain A residue 2093 CYS Chi-restraints excluded: chain A residue 2094 MET Chi-restraints excluded: chain A residue 2341 LEU Chi-restraints excluded: chain A residue 2342 CYS Chi-restraints excluded: chain A residue 2352 HIS Chi-restraints excluded: chain A residue 2915 ARG Chi-restraints excluded: chain A residue 3218 MET Chi-restraints excluded: chain A residue 3363 SER Chi-restraints excluded: chain A residue 3591 ASP Chi-restraints excluded: chain A residue 3664 ASN Chi-restraints excluded: chain A residue 4087 HIS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 298 optimal weight: 7.9990 chunk 244 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 359 optimal weight: 0.9990 chunk 388 optimal weight: 0.7980 chunk 320 optimal weight: 0.7980 chunk 356 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: