Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 03:26:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/04_2023/8de8_27387_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/04_2023/8de8_27387.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/04_2023/8de8_27387_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/04_2023/8de8_27387_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/04_2023/8de8_27387_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/04_2023/8de8_27387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/04_2023/8de8_27387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/04_2023/8de8_27387_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8de8_27387/04_2023/8de8_27387_updated.pdb" } resolution = 2.82 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 ------------------------------------------------------------------------------- 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= 0.002 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 4 5.49 5 S 16 5.16 5 C 3014 2.51 5 N 676 2.21 5 O 784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 4498 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2168 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 7, 'TRANS': 268} Chain: "A" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2168 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 7, 'TRANS': 268} Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'D21': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 83 Unusual residues: {' K': 4, 'D21': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 2.90, per 1000 atoms: 0.64 Number of scatterers: 4498 At special positions: 0 Unit cell: (90.738, 85.626, 94.572, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 16 16.00 P 4 15.00 O 784 8.00 N 676 7.00 C 3014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS A 93 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 667.3 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 0 sheets defined 75.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 44 through 90 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 96 through 111 Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 153 through 198 Proline residue: B 168 - end of helix removed outlier: 4.826A pdb=" N LYS B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 222 Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.735A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 Processing helix chain 'B' and resid 270 through 314 removed outlier: 3.656A pdb=" N ALA B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 90 Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 153 through 198 Proline residue: A 168 - end of helix removed outlier: 4.826A pdb=" N LYS A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 222 Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.735A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 Processing helix chain 'A' and resid 270 through 314 removed outlier: 3.657A pdb=" N ALA A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 1002 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: 1.14 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 676 1.32 - 1.44: 1268 1.44 - 1.57: 2618 1.57 - 1.70: 12 1.70 - 1.83: 26 Bond restraints: 4600 Sorted by residual: bond pdb=" C33 D21 A 402 " pdb=" C34 D21 A 402 " ideal model delta sigma weight residual 1.532 1.585 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C33 D21 B 402 " pdb=" C34 D21 B 402 " ideal model delta sigma weight residual 1.532 1.584 -0.052 2.00e-02 2.50e+03 6.83e+00 bond pdb=" C33 D21 A 401 " pdb=" C34 D21 A 401 " ideal model delta sigma weight residual 1.532 1.584 -0.052 2.00e-02 2.50e+03 6.78e+00 bond pdb=" C33 D21 B 401 " pdb=" C34 D21 B 401 " ideal model delta sigma weight residual 1.532 1.583 -0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" C ILE B 299 " pdb=" O ILE B 299 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.23e-02 6.61e+03 5.65e+00 ... (remaining 4595 not shown) Histogram of bond angle deviations from ideal: 98.87 - 110.34: 946 110.34 - 121.81: 4493 121.81 - 133.29: 749 133.29 - 144.76: 14 144.76 - 156.23: 8 Bond angle restraints: 6210 Sorted by residual: angle pdb=" C40 D21 A 402 " pdb=" C41 D21 A 402 " pdb=" C42 D21 A 402 " ideal model delta sigma weight residual 120.01 156.23 -36.22 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C40 D21 B 402 " pdb=" C41 D21 B 402 " pdb=" C42 D21 B 402 " ideal model delta sigma weight residual 120.01 156.17 -36.16 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C39 D21 B 402 " pdb=" C40 D21 B 402 " pdb=" C41 D21 B 402 " ideal model delta sigma weight residual 120.02 156.11 -36.09 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C39 D21 A 402 " pdb=" C40 D21 A 402 " pdb=" C41 D21 A 402 " ideal model delta sigma weight residual 120.02 156.05 -36.03 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C39 D21 B 401 " pdb=" C40 D21 B 401 " pdb=" C41 D21 B 401 " ideal model delta sigma weight residual 120.02 154.72 -34.70 3.00e+00 1.11e-01 1.34e+02 ... (remaining 6205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.09: 2517 31.09 - 62.18: 106 62.18 - 93.28: 20 93.28 - 124.37: 0 124.37 - 155.46: 2 Dihedral angle restraints: 2645 sinusoidal: 1075 harmonic: 1570 Sorted by residual: dihedral pdb=" C06 D21 A 402 " pdb=" C07 D21 A 402 " pdb=" C08 D21 A 402 " pdb=" C09 D21 A 402 " ideal model delta sinusoidal sigma weight residual -134.99 20.47 -155.46 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C06 D21 B 402 " pdb=" C07 D21 B 402 " pdb=" C08 D21 B 402 " pdb=" C09 D21 B 402 " ideal model delta sinusoidal sigma weight residual -134.99 20.47 -155.46 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" CG ARG B 111 " pdb=" CD ARG B 111 " pdb=" NE ARG B 111 " pdb=" CZ ARG B 111 " ideal model delta sinusoidal sigma weight residual 180.00 135.77 44.23 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 2642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 581 0.065 - 0.129: 103 0.129 - 0.193: 24 0.193 - 0.258: 0 0.258 - 0.322: 2 Chirality restraints: 710 Sorted by residual: chirality pdb=" CB ILE B 264 " pdb=" CA ILE B 264 " pdb=" CG1 ILE B 264 " pdb=" CG2 ILE B 264 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE A 264 " pdb=" CA ILE A 264 " pdb=" CG1 ILE A 264 " pdb=" CG2 ILE A 264 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB VAL B 41 " pdb=" CA VAL B 41 " pdb=" CG1 VAL B 41 " pdb=" CG2 VAL B 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 707 not shown) Planarity restraints: 742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 271 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO B 272 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 271 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO A 272 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 149 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO B 150 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " 0.033 5.00e-02 4.00e+02 ... (remaining 739 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 960 2.79 - 3.38: 5333 3.38 - 3.96: 8330 3.96 - 4.55: 11373 4.55 - 5.14: 16843 Nonbonded interactions: 42839 Sorted by model distance: nonbonded pdb=" O ARG B 297 " pdb=" OG SER B 300 " model vdw 2.200 2.440 nonbonded pdb=" O GLY B 137 " pdb=" OG1 THR B 141 " model vdw 2.205 2.440 nonbonded pdb=" O GLY A 137 " pdb=" OG1 THR A 141 " model vdw 2.205 2.440 nonbonded pdb=" O ARG A 297 " pdb=" OG SER A 300 " model vdw 2.248 2.440 nonbonded pdb=" OE1 GLN A 76 " pdb=" NH2 ARG A 79 " model vdw 2.305 2.520 ... (remaining 42834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 315 or resid 401 through 402)) selection = chain 'B' } 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: 0.290 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: 1.890 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.240 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.006 0.053 4600 Z= 0.371 Angle : 1.628 36.221 6210 Z= 0.661 Chirality : 0.054 0.322 710 Planarity : 0.008 0.064 742 Dihedral : 17.712 155.459 1638 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.33), residues: 548 helix: 2.16 (0.23), residues: 436 sheet: None (None), residues: 0 loop : -1.13 (0.52), residues: 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 193 time to evaluate : 0.492 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 195 average time/residue: 0.8889 time to fit residues: 181.1209 Evaluate side-chains 133 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.9915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 0.0020 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN B 95 GLN B 115 ASN B 122 GLN B 313 HIS A 76 GLN A 95 GLN A 115 ASN A 122 GLN A 313 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 4600 Z= 0.247 Angle : 0.729 11.577 6210 Z= 0.356 Chirality : 0.040 0.133 710 Planarity : 0.005 0.041 742 Dihedral : 16.638 175.174 680 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 3.88 % 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: 3.31 (0.36), residues: 548 helix: 3.03 (0.24), residues: 436 sheet: None (None), residues: 0 loop : -1.51 (0.53), residues: 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.538 Fit side-chains outliers start: 18 outliers final: 4 residues processed: 149 average time/residue: 0.9690 time to fit residues: 150.4323 Evaluate side-chains 135 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0887 time to fit residues: 0.9214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 0.0470 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN A 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2905 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: