Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 03:31:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/04_2023/7p2q_13172_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/04_2023/7p2q_13172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/04_2023/7p2q_13172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/04_2023/7p2q_13172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/04_2023/7p2q_13172_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p2q_13172/04_2023/7p2q_13172_neut.pdb" } resolution = 4.9 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3106 2.51 5 N 778 2.21 5 O 873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 4780 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain: "B" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1426 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "C" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1411 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "D" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 696 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.01, per 1000 atoms: 0.63 Number of scatterers: 4780 At special positions: 0 Unit cell: (81.81, 84.24, 126.36, 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 23 16.00 O 873 8.00 N 778 7.00 C 3106 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 - 3.50 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 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN B 141 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 666.7 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 6 sheets defined 41.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 26 through 56 removed outlier: 4.288A pdb=" N LEU A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.782A pdb=" N VAL A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 33 Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 79 through 105 Processing helix chain 'C' and resid 106 through 109 removed outlier: 3.516A pdb=" N GLU C 109 " --> pdb=" O PRO C 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 106 through 109' Processing helix chain 'C' and resid 110 through 136 removed outlier: 3.720A pdb=" N LEU C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 207 through 224 removed outlier: 3.700A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.653A pdb=" N LEU D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 109 Processing helix chain 'D' and resid 112 through 131 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.601A pdb=" N LEU D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 3.983A pdb=" N ASP A 77 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99 removed outlier: 5.282A pdb=" N VAL A 110 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS A 126 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 112 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.094A pdb=" N VAL B 51 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 63 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP B 53 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER B 61 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 129 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.679A pdb=" N GLN B 84 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 104 Processing sheet with id=AA6, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.622A pdb=" N LEU C 159 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C 142 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TRP C 157 " --> pdb=" O VAL C 142 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 693 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: 1.09 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1460 1.34 - 1.46: 971 1.46 - 1.58: 2424 1.58 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 4896 Sorted by residual: bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.567 -0.048 2.00e-02 2.50e+03 5.76e+00 bond pdb=" C1 MAN E 4 " pdb=" C2 MAN E 4 " ideal model delta sigma weight residual 1.526 1.563 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" C1 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sigma weight residual 1.410 1.445 -0.035 2.00e-02 2.50e+03 2.99e+00 bond pdb=" C5 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.418 1.452 -0.034 2.00e-02 2.50e+03 2.94e+00 bond pdb=" C LEU D 131 " pdb=" N PRO D 132 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.18e-02 7.18e+03 2.88e+00 ... (remaining 4891 not shown) Histogram of bond angle deviations from ideal: 100.72 - 107.41: 182 107.41 - 114.10: 2765 114.10 - 120.79: 2047 120.79 - 127.48: 1585 127.48 - 134.17: 50 Bond angle restraints: 6629 Sorted by residual: angle pdb=" C LYS B 121 " pdb=" N ASP B 122 " pdb=" CA ASP B 122 " ideal model delta sigma weight residual 121.54 131.00 -9.46 1.91e+00 2.74e-01 2.45e+01 angle pdb=" C GLY B 133 " pdb=" N ASN B 134 " pdb=" CA ASN B 134 " ideal model delta sigma weight residual 121.54 130.70 -9.16 1.91e+00 2.74e-01 2.30e+01 angle pdb=" C GLU A 58 " pdb=" N SER A 59 " pdb=" CA SER A 59 " ideal model delta sigma weight residual 121.80 130.19 -8.39 2.44e+00 1.68e-01 1.18e+01 angle pdb=" N SER A 59 " pdb=" CA SER A 59 " pdb=" C SER A 59 " ideal model delta sigma weight residual 109.81 116.82 -7.01 2.21e+00 2.05e-01 1.00e+01 angle pdb=" CA LEU D 75 " pdb=" CB LEU D 75 " pdb=" CG LEU D 75 " ideal model delta sigma weight residual 116.30 125.83 -9.53 3.50e+00 8.16e-02 7.42e+00 ... (remaining 6624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.01: 2726 14.01 - 28.02: 104 28.02 - 42.03: 38 42.03 - 56.04: 0 56.04 - 70.05: 1 Dihedral angle restraints: 2869 sinusoidal: 1161 harmonic: 1708 Sorted by residual: dihedral pdb=" CA ASP C 154 " pdb=" C ASP C 154 " pdb=" N ASP C 155 " pdb=" CA ASP C 155 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA TYR B 174 " pdb=" C TYR B 174 " pdb=" N GLU B 175 " pdb=" CA GLU B 175 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER D 74 " pdb=" C SER D 74 " pdb=" N LEU D 75 " pdb=" CA LEU D 75 " ideal model delta harmonic sigma weight residual -180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 2866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 590 0.057 - 0.114: 138 0.114 - 0.171: 22 0.171 - 0.228: 5 0.228 - 0.285: 1 Chirality restraints: 756 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE B 109 " pdb=" CA ILE B 109 " pdb=" CG1 ILE B 109 " pdb=" CG2 ILE B 109 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN B 134 " pdb=" N ASN B 134 " pdb=" C ASN B 134 " pdb=" CB ASN B 134 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 753 not shown) Planarity restraints: 822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 140 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO D 141 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 70 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 71 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 37 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 38 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " -0.026 5.00e-02 4.00e+02 ... (remaining 819 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1005 2.79 - 3.32: 4108 3.32 - 3.85: 7306 3.85 - 4.37: 7850 4.37 - 4.90: 13680 Nonbonded interactions: 33949 Sorted by model distance: nonbonded pdb=" NH1 ARG A 109 " pdb=" CE1 PHE B 86 " model vdw 2.264 3.420 nonbonded pdb=" O LYS B 121 " pdb=" OD1 ASP B 122 " model vdw 2.290 3.040 nonbonded pdb=" NH1 ARG C 84 " pdb=" OE2 GLU C 136 " model vdw 2.352 2.520 nonbonded pdb=" OG SER B 90 " pdb=" O THR B 145 " model vdw 2.357 2.440 nonbonded pdb=" OD1 ASP A 120 " pdb=" NZ LYS A 147 " model vdw 2.401 2.520 ... (remaining 33944 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 group one per residue 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: 0.320 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: 2.050 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.020 Find NCS groups from input model: 0.130 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 0.048 4896 Z= 0.243 Angle : 0.840 9.532 6629 Z= 0.432 Chirality : 0.051 0.285 756 Planarity : 0.007 0.057 821 Dihedral : 8.761 70.055 1767 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.00 % 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: -3.09 (0.29), residues: 579 helix: -1.26 (0.24), residues: 220 sheet: -1.18 (0.47), residues: 120 loop : -3.26 (0.32), residues: 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 0.651 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 outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2168 time to fit residues: 69.4840 Evaluate side-chains 146 residues out of total 521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4974 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: