Starting phenix.real_space_refine on Fri Jan 19 06:37:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbh_30631/01_2024/7dbh_30631.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbh_30631/01_2024/7dbh_30631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbh_30631/01_2024/7dbh_30631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbh_30631/01_2024/7dbh_30631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbh_30631/01_2024/7dbh_30631.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dbh_30631/01_2024/7dbh_30631.pdb" } resolution = 3.6 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= 0.001 sd= 0.004 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 250 5.49 5 S 14 5.16 5 C 5902 2.51 5 N 1973 2.21 5 O 2492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10631 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 726 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 677 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 740 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2563 Classifications: {'DNA': 126} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 125} Chain: "J" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2597 Classifications: {'DNA': 126} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 125} Time building chain proxies: 5.86, per 1000 atoms: 0.55 Number of scatterers: 10631 At special positions: 0 Unit cell: (122.1, 75.9, 115.5, 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 14 16.00 P 250 15.00 O 2492 8.00 N 1973 7.00 C 5902 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 Time building additional restraints: 6.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 76.8% alpha, 2.9% beta 116 base pairs and 191 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.717A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.608A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.314A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 49 through 57 removed outlier: 3.638A pdb=" N SER E 57 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 47 through 76 removed outlier: 4.151A pdb=" N TYR F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.383A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.824A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.777A pdb=" N CYS A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.821A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.864A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.435A pdb=" N CYS E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.257A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 403 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 303 hydrogen bonds 594 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 191 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 7.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2284 1.33 - 1.45: 3447 1.45 - 1.57: 5077 1.57 - 1.69: 500 1.69 - 1.81: 22 Bond restraints: 11330 Sorted by residual: bond pdb=" N ILE E 130 " pdb=" CA ILE E 130 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.14e-02 7.69e+03 8.54e+00 bond pdb=" N ARG A 63 " pdb=" CA ARG A 63 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.54e+00 bond pdb=" N ARG G 42 " pdb=" CA ARG G 42 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.23e-02 6.61e+03 6.18e+00 bond pdb=" N GLY H 32 " pdb=" CA GLY H 32 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.17e+00 bond pdb=" N CYS E 131 " pdb=" CA CYS E 131 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.03e+00 ... (remaining 11325 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.53: 1156 105.53 - 112.32: 6148 112.32 - 119.11: 3151 119.11 - 125.90: 5146 125.90 - 132.69: 784 Bond angle restraints: 16385 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.71 109.21 4.50 9.50e-01 1.11e+00 2.25e+01 angle pdb=" O CYS E 131 " pdb=" C CYS E 131 " pdb=" N ARG E 132 " ideal model delta sigma weight residual 122.12 125.71 -3.59 1.06e+00 8.90e-01 1.15e+01 angle pdb=" C ARG A 132 " pdb=" CA ARG A 132 " pdb=" CB ARG A 132 " ideal model delta sigma weight residual 110.10 116.35 -6.25 1.90e+00 2.77e-01 1.08e+01 angle pdb=" N ARG C 17 " pdb=" CA ARG C 17 " pdb=" C ARG C 17 " ideal model delta sigma weight residual 113.43 109.44 3.99 1.26e+00 6.30e-01 1.00e+01 angle pdb=" N ARG B 55 " pdb=" CA ARG B 55 " pdb=" C ARG B 55 " ideal model delta sigma weight residual 111.28 107.92 3.36 1.09e+00 8.42e-01 9.51e+00 ... (remaining 16380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.66: 4874 33.66 - 67.32: 1205 67.32 - 100.98: 41 100.98 - 134.65: 5 134.65 - 168.31: 5 Dihedral angle restraints: 6130 sinusoidal: 4116 harmonic: 2014 Sorted by residual: dihedral pdb=" C ARG A 132 " pdb=" N ARG A 132 " pdb=" CA ARG A 132 " pdb=" CB ARG A 132 " ideal model delta harmonic sigma weight residual -122.60 -133.04 10.44 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 51.69 168.31 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC J -58 " pdb=" C3' DC J -58 " pdb=" O3' DC J -58 " pdb=" P DT J -57 " ideal model delta sinusoidal sigma weight residual 220.00 51.95 168.05 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 6127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1510 0.060 - 0.120: 349 0.120 - 0.180: 14 0.180 - 0.241: 0 0.241 - 0.301: 1 Chirality restraints: 1874 Sorted by residual: chirality pdb=" CA ARG A 132 " pdb=" N ARG A 132 " pdb=" C ARG A 132 " pdb=" CB ARG A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA LEU E 100 " pdb=" N LEU E 100 " pdb=" C LEU E 100 " pdb=" CB LEU E 100 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CA LEU F 37 " pdb=" N LEU F 37 " pdb=" C LEU F 37 " pdb=" CB LEU F 37 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 1871 not shown) Planarity restraints: 1197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -36 " 0.016 2.00e-02 2.50e+03 1.08e-02 3.50e+00 pdb=" N9 DG J -36 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DG J -36 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG J -36 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG J -36 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG J -36 " -0.021 2.00e-02 2.50e+03 pdb=" O6 DG J -36 " 0.015 2.00e-02 2.50e+03 pdb=" N1 DG J -36 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG J -36 " 0.008 2.00e-02 2.50e+03 pdb=" N2 DG J -36 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG J -36 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG J -36 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 35 " -0.007 2.00e-02 2.50e+03 1.20e-02 3.22e+00 pdb=" N1 DC I 35 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DC I 35 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DC I 35 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DC I 35 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC I 35 " 0.028 2.00e-02 2.50e+03 pdb=" N4 DC I 35 " -0.017 2.00e-02 2.50e+03 pdb=" C5 DC I 35 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 6 " -0.022 2.00e-02 2.50e+03 1.16e-02 3.05e+00 pdb=" N1 DC I 6 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DC I 6 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DC I 6 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 6 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 6 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC I 6 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 6 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC I 6 " 0.003 2.00e-02 2.50e+03 ... (remaining 1194 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 1 2.14 - 2.83: 3202 2.83 - 3.52: 18486 3.52 - 4.21: 29919 4.21 - 4.90: 44435 Nonbonded interactions: 96043 Sorted by model distance: nonbonded pdb=" O ALA F 33 " pdb=" CD2 LEU F 37 " model vdw 1.451 3.460 nonbonded pdb=" O HIS H 109 " pdb=" OG SER H 112 " model vdw 2.160 2.440 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.166 2.440 nonbonded pdb=" N2 DG I 58 " pdb=" O2 DT J -57 " model vdw 2.204 2.520 nonbonded pdb=" N2 DG I -60 " pdb=" O2 DC J 61 " model vdw 2.206 2.520 ... (remaining 96038 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' selection = (chain 'E' and resid 55 through 132) } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 109) } ncs_group { reference = (chain 'D' and (resid 33 through 123 or (resid 124 and (name N or name CA or nam \ e C or name CB or name OG )))) selection = (chain 'H' and resid 33 through 124) } 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: 0.250 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: 1.860 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 36.690 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 0.007 0.042 11330 Z= 0.417 Angle : 0.740 6.252 16385 Z= 0.488 Chirality : 0.047 0.301 1874 Planarity : 0.003 0.019 1197 Dihedral : 28.574 168.307 4834 Min Nonbonded Distance : 1.451 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.65 % Cbeta Deviations : 0.15 % 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: 0.54 (0.31), residues: 681 helix: 1.01 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.62 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS C 31 PHE 0.009 0.002 PHE C 25 TYR 0.017 0.002 TYR D 83 ARG 0.013 0.001 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 0.778 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PRO C 109 " (corrupted residue). Skipping it. Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable