Starting phenix.real_space_refine on Wed Dec 13 18:04:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhx_24470/12_2023/7rhx_24470.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhx_24470/12_2023/7rhx_24470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhx_24470/12_2023/7rhx_24470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhx_24470/12_2023/7rhx_24470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhx_24470/12_2023/7rhx_24470.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhx_24470/12_2023/7rhx_24470.pdb" } resolution = 3.23 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= 0.081 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 P 168 5.49 5 S 60 5.16 5 C 7970 2.51 5 N 2562 2.21 5 O 2868 1.98 5 H 12159 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 25787 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 5110 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 7, 'TRANS': 314} Chain: "B" Number of atoms: 5111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 5111 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 7, 'TRANS': 314} Chain: "C" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 1329 Classifications: {'DNA': 42} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 41} Chain: "D" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 1344 Classifications: {'DNA': 42} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 41} Chain: "E" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 1329 Classifications: {'DNA': 42} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 41} Chain: "F" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 1344 Classifications: {'DNA': 42} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 41} Chain: "G" Number of atoms: 5110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 5110 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 7, 'TRANS': 314} Chain: "H" Number of atoms: 5110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 5110 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 7, 'TRANS': 314} Time building chain proxies: 11.98, per 1000 atoms: 0.46 Number of scatterers: 25787 At special positions: 0 Unit cell: (87.203, 164.517, 180.699, 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) S 60 16.00 P 168 15.00 O 2868 8.00 N 2562 7.00 C 7970 6.00 H 12159 1.00 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: 20.08 Conformation dependent library (CDL) restraints added in 2.3 seconds 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 5 sheets defined 68.8% alpha, 2.3% beta 84 base pairs and 147 stacking pairs defined. Time for finding SS restraints: 11.54 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.633A pdb=" N ARG A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 38 through 59 removed outlier: 3.696A pdb=" N MET A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 47 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.883A pdb=" N ASP A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 103 Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 110 through 127 removed outlier: 3.672A pdb=" N SER A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 179 through 180 No H-bonds generated for 'chain 'A' and resid 179 through 180' Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 214 through 229 removed outlier: 3.782A pdb=" N LEU A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 removed outlier: 3.981A pdb=" N ASP A 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.519A pdb=" N GLY A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 305 through 314 removed outlier: 3.566A pdb=" N ALA A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 4.422A pdb=" N VAL A 321 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 341 removed outlier: 4.459A pdb=" N VAL A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 34 through 37 Processing helix chain 'B' and resid 38 through 59 removed outlier: 3.501A pdb=" N TRP B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 81 removed outlier: 3.645A pdb=" N ARG B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 103 removed outlier: 3.839A pdb=" N LEU B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 109 Processing helix chain 'B' and resid 110 through 127 removed outlier: 3.777A pdb=" N VAL B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 154 through 171 Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 179 through 180 No H-bonds generated for 'chain 'B' and resid 179 through 180' Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 214 through 229 Processing helix chain 'B' and resid 230 through 233 removed outlier: 3.726A pdb=" N ASP B 233 " --> pdb=" O VAL B 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 230 through 233' Processing helix chain 'B' and resid 257 through 274 removed outlier: 3.580A pdb=" N PHE B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 303 Processing helix chain 'B' and resid 305 through 314 Processing helix chain 'B' and resid 318 through 325 removed outlier: 3.708A pdb=" N MET B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 333 through 340 Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 34 through 37 Processing helix chain 'G' and resid 38 through 59 removed outlier: 3.599A pdb=" N MET G 44 " --> pdb=" O HIS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 81 removed outlier: 3.550A pdb=" N ARG G 81 " --> pdb=" O TYR G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 103 removed outlier: 3.553A pdb=" N LEU G 95 " --> pdb=" O HIS G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 109 Processing helix chain 'G' and resid 110 through 127 removed outlier: 3.772A pdb=" N SER G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 154 through 171 removed outlier: 3.513A pdb=" N ASN G 160 " --> pdb=" O GLN G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 179 removed outlier: 3.513A pdb=" N ARG G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 183 No H-bonds generated for 'chain 'G' and resid 181 through 183' Processing helix chain 'G' and resid 214 through 228 removed outlier: 3.538A pdb=" N ARG G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 233 removed outlier: 3.585A pdb=" N ASP G 233 " --> pdb=" O VAL G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 274 removed outlier: 3.657A pdb=" N ILE G 264 " --> pdb=" O ALA G 260 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE G 265 " --> pdb=" O LEU G 261 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE G 272 " --> pdb=" O THR G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 302 removed outlier: 3.556A pdb=" N ALA G 302 " --> pdb=" O ASP G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 314 Processing helix chain 'G' and resid 317 through 326 removed outlier: 4.380A pdb=" N VAL G 321 " --> pdb=" O ASN G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 332 Processing helix chain 'G' and resid 333 through 340 removed outlier: 3.540A pdb=" N ARG G 337 " --> pdb=" O GLY G 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 33 Processing helix chain 'H' and resid 34 through 37 Processing helix chain 'H' and resid 38 through 59 removed outlier: 3.703A pdb=" N TRP H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS H 43 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET H 44 " --> pdb=" O HIS H 40 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU H 45 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER H 51 " --> pdb=" O SER H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.653A pdb=" N ASP H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 103 removed outlier: 3.728A pdb=" N LEU H 95 " --> pdb=" O HIS H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 109 removed outlier: 3.605A pdb=" N ASP H 109 " --> pdb=" O ARG H 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 109' Processing helix chain 'H' and resid 110 through 127 removed outlier: 3.628A pdb=" N ARG H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 150 Processing helix chain 'H' and resid 154 through 171 Processing helix chain 'H' and resid 173 through 178 Processing helix chain 'H' and resid 179 through 180 No H-bonds generated for 'chain 'H' and resid 179 through 180' Processing helix chain 'H' and resid 181 through 183 No H-bonds generated for 'chain 'H' and resid 181 through 183' Processing helix chain 'H' and resid 216 through 229 removed outlier: 4.068A pdb=" N LEU H 220 " --> pdb=" O GLY H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 233 removed outlier: 3.863A pdb=" N ASP H 233 " --> pdb=" O VAL H 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 230 through 233' Processing helix chain 'H' and resid 257 through 274 removed outlier: 3.936A pdb=" N GLY H 263 " --> pdb=" O ARG H 259 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE H 265 " --> pdb=" O LEU H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 302 Processing helix chain 'H' and resid 305 through 314 Processing helix chain 'H' and resid 318 through 325 removed outlier: 4.121A pdb=" N MET H 322 " --> pdb=" O VAL H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 328 No H-bonds generated for 'chain 'H' and resid 326 through 328' Processing helix chain 'H' and resid 329 through 332 Processing helix chain 'H' and resid 333 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AA3, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AA4, first strand: chain 'H' and resid 185 through 187 Processing sheet with id=AA5, first strand: chain 'H' and resid 241 through 242 removed outlier: 4.512A pdb=" N ARG H 241 " --> pdb=" O ALA H 249 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 202 hydrogen bonds 404 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 147 stacking parallelities Total time for adding SS restraints: 10.04 Time building geometry restraints manager: 20.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12143 1.03 - 1.23: 102 1.23 - 1.42: 6083 1.42 - 1.61: 7933 1.61 - 1.81: 106 Bond restraints: 26367 Sorted by residual: bond pdb=" N SER G 20 " pdb=" CA SER G 20 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N SER H 20 " pdb=" CA SER H 20 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" N SER B 20 " pdb=" CA SER B 20 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" N SER A 20 " pdb=" CA SER A 20 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" C4' DC C 15 " pdb=" O4' DC C 15 " ideal model delta sigma weight residual 1.450 1.419 0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 26362 not shown) Histogram of bond angle deviations from ideal: 97.66 - 104.93: 733 104.93 - 112.21: 28699 112.21 - 119.48: 7547 119.48 - 126.76: 9969 126.76 - 134.03: 596 Bond angle restraints: 47544 Sorted by residual: angle pdb=" C3' DT E 34 " pdb=" O3' DT E 34 " pdb=" P DC E 35 " ideal model delta sigma weight residual 120.20 126.34 -6.14 1.50e+00 4.44e-01 1.67e+01 angle pdb=" C4' DC F 21 " pdb=" O4' DC F 21 " pdb=" C1' DC F 21 " ideal model delta sigma weight residual 109.70 103.66 6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" C3' DG E 14 " pdb=" O3' DG E 14 " pdb=" P DC E 15 " ideal model delta sigma weight residual 120.20 125.74 -5.54 1.50e+00 4.44e-01 1.37e+01 angle pdb=" O3' DG C 14 " pdb=" C3' DG C 14 " pdb=" C2' DG C 14 " ideal model delta sigma weight residual 111.50 116.82 -5.32 1.50e+00 4.44e-01 1.26e+01 angle pdb=" O3' DC E 15 " pdb=" C3' DC E 15 " pdb=" C2' DC E 15 " ideal model delta sigma weight residual 111.50 116.80 -5.30 1.50e+00 4.44e-01 1.25e+01 ... (remaining 47539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 10563 34.87 - 69.73: 866 69.73 - 104.60: 12 104.60 - 139.47: 0 139.47 - 174.33: 4 Dihedral angle restraints: 11445 sinusoidal: 7212 harmonic: 4233 Sorted by residual: dihedral pdb=" CA THR B 206 " pdb=" C THR B 206 " pdb=" N ALA B 207 " pdb=" CA ALA B 207 " ideal model delta harmonic sigma weight residual 180.00 152.39 27.61 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA LYS A 62 " pdb=" C LYS A 62 " pdb=" N TRP A 63 " pdb=" CA TRP A 63 " ideal model delta harmonic sigma weight residual -180.00 -158.14 -21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LYS B 62 " pdb=" C LYS B 62 " pdb=" N TRP B 63 " pdb=" CA TRP B 63 " ideal model delta harmonic sigma weight residual 180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 11442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1810 0.057 - 0.113: 351 0.113 - 0.170: 48 0.170 - 0.227: 5 0.227 - 0.284: 2 Chirality restraints: 2216 Sorted by residual: chirality pdb=" C3' DC E 15 " pdb=" C4' DC E 15 " pdb=" O3' DC E 15 " pdb=" C2' DC E 15 " both_signs ideal model delta sigma weight residual False -2.66 -2.38 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' DT E 34 " pdb=" C4' DT E 34 " pdb=" O3' DT E 34 " pdb=" C2' DT E 34 " both_signs ideal model delta sigma weight residual False -2.66 -2.40 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C1' DT C 31 " pdb=" O4' DT C 31 " pdb=" C2' DT C 31 " pdb=" N1 DT C 31 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2213 not shown) Planarity restraints: 3358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 124 " 0.035 2.00e-02 2.50e+03 4.27e-02 2.74e+01 pdb=" CG ASN G 124 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN G 124 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN G 124 " -0.067 2.00e-02 2.50e+03 pdb="HD21 ASN G 124 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN G 124 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG E 36 " -0.053 2.00e-02 2.50e+03 2.35e-02 1.93e+01 pdb=" N9 DG E 36 " 0.068 2.00e-02 2.50e+03 pdb=" C8 DG E 36 " -0.008 2.00e-02 2.50e+03 pdb=" N7 DG E 36 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG E 36 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG E 36 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG E 36 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG E 36 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG E 36 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG E 36 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG E 36 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG E 36 " 0.005 2.00e-02 2.50e+03 pdb=" H8 DG E 36 " 0.002 2.00e-02 2.50e+03 pdb=" H1 DG E 36 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 31 " 0.052 2.00e-02 2.50e+03 2.50e-02 1.87e+01 pdb=" N1 DT C 31 " -0.067 2.00e-02 2.50e+03 pdb=" C2 DT C 31 " 0.011 2.00e-02 2.50e+03 pdb=" O2 DT C 31 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT C 31 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT C 31 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT C 31 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT C 31 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT C 31 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DT C 31 " -0.007 2.00e-02 2.50e+03 pdb=" H3 DT C 31 " 0.002 2.00e-02 2.50e+03 pdb=" H6 DT C 31 " -0.006 2.00e-02 2.50e+03 ... (remaining 3355 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 789 2.17 - 2.78: 44887 2.78 - 3.39: 63554 3.39 - 3.99: 82968 3.99 - 4.60: 132221 Nonbonded interactions: 324419 Sorted by model distance: nonbonded pdb=" HG SER B 257 " pdb=" OP2 DT C 6 " model vdw 1.567 1.850 nonbonded pdb=" HG SER B 205 " pdb=" O ALA B 207 " model vdw 1.596 1.850 nonbonded pdb=" O LEU B 215 " pdb=" HG1 THR B 218 " model vdw 1.614 1.850 nonbonded pdb=" HG SER A 287 " pdb=" OP1 DA C 25 " model vdw 1.627 1.850 nonbonded pdb="HH12 ARG G 187 " pdb=" OE2 GLU G 222 " model vdw 1.641 1.850 ... (remaining 324414 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 'B' and (resid 20 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 341)) selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 1.010 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: 0.330 Extract box with map and model: 5.050 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 86.550 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 0.039 14208 Z= 0.244 Angle : 0.790 7.267 19904 Z= 0.509 Chirality : 0.046 0.284 2216 Planarity : 0.012 0.110 1984 Dihedral : 20.665 174.333 5768 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -0.38 (0.22), residues: 1280 helix: -0.34 (0.17), residues: 772 sheet: -0.99 (0.62), residues: 68 loop : 0.44 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP H 315 HIS 0.007 0.002 HIS B 99 PHE 0.021 0.002 PHE A 31 TYR 0.016 0.004 TYR G 237 ARG 0.023 0.002 ARG B 292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.8276 time to fit residues: 174.8884 Evaluate side-chains 90 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: