Starting phenix.real_space_refine on Tue Mar 19 23:43:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhx_24470/03_2024/7rhx_24470.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhx_24470/03_2024/7rhx_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_24470/03_2024/7rhx_24470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhx_24470/03_2024/7rhx_24470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhx_24470/03_2024/7rhx_24470.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhx_24470/03_2024/7rhx_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.31, per 1000 atoms: 0.48 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: 22.20 Conformation dependent library (CDL) restraints added in 2.4 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: 11.62 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: 11.94 Time building geometry restraints manager: 23.02 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: 10707 34.87 - 69.73: 954 69.73 - 104.60: 12 104.60 - 139.47: 0 139.47 - 174.33: 4 Dihedral angle restraints: 11677 sinusoidal: 7444 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 11674 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.350 Extract box with map and model: 5.160 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 95.530 Find NCS groups from input model: 1.110 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: 0.000 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: 106.400 ------------------------------------------------------------------------------- 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 : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.8335 (tpt) cc_final: 0.8119 (tpt) REVERT: G 25 LYS cc_start: 0.8920 (mttt) cc_final: 0.8710 (ttpp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.7562 time to fit residues: 160.5744 Evaluate side-chains 91 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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: 5.9990 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14208 Z= 0.283 Angle : 0.639 7.260 19904 Z= 0.385 Chirality : 0.040 0.143 2216 Planarity : 0.004 0.038 1984 Dihedral : 24.036 163.692 3320 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.37 % Allowed : 4.48 % Favored : 95.15 % 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: 0.92 (0.23), residues: 1280 helix: 1.03 (0.18), residues: 792 sheet: -1.49 (0.59), residues: 68 loop : 0.42 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 63 HIS 0.006 0.001 HIS H 289 PHE 0.015 0.002 PHE B 265 TYR 0.011 0.001 TYR H 77 ARG 0.008 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 2 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 98 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.796 Fit side-chains revert: symmetry clash REVERT: G 28 MET cc_start: 0.8573 (mmm) cc_final: 0.8314 (mmp) outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 0.5258 time to fit residues: 76.0792 Evaluate side-chains 83 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain H residue 200 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 8.9990 chunk 40 optimal weight: 0.0070 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14208 Z= 0.279 Angle : 0.610 7.075 19904 Z= 0.368 Chirality : 0.039 0.131 2216 Planarity : 0.004 0.036 1984 Dihedral : 24.023 163.044 3320 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.65 % Allowed : 5.69 % Favored : 93.66 % 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: 1.08 (0.24), residues: 1280 helix: 1.36 (0.19), residues: 788 sheet: -1.78 (0.57), residues: 68 loop : 0.12 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 52 HIS 0.004 0.001 HIS A 99 PHE 0.013 0.001 PHE B 64 TYR 0.009 0.001 TYR B 324 ARG 0.003 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 3 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 91 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 1.742 Fit side-chains REVERT: G 28 MET cc_start: 0.8609 (mmm) cc_final: 0.8309 (mmp) outliers start: 7 outliers final: 4 residues processed: 88 average time/residue: 0.5123 time to fit residues: 68.7610 Evaluate side-chains 84 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14208 Z= 0.252 Angle : 0.584 6.848 19904 Z= 0.352 Chirality : 0.038 0.129 2216 Planarity : 0.003 0.030 1984 Dihedral : 24.069 163.306 3320 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.75 % Allowed : 7.28 % Favored : 91.98 % 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: 1.10 (0.24), residues: 1280 helix: 1.48 (0.19), residues: 790 sheet: -1.97 (0.58), residues: 68 loop : -0.10 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 52 HIS 0.003 0.001 HIS A 99 PHE 0.011 0.001 PHE B 64 TYR 0.011 0.001 TYR H 77 ARG 0.003 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 4 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 89 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 1.718 Fit side-chains REVERT: G 28 MET cc_start: 0.8595 (mmm) cc_final: 0.8332 (mmp) outliers start: 8 outliers final: 6 residues processed: 85 average time/residue: 0.4985 time to fit residues: 64.9257 Evaluate side-chains 89 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14208 Z= 0.333 Angle : 0.621 7.204 19904 Z= 0.373 Chirality : 0.041 0.136 2216 Planarity : 0.004 0.038 1984 Dihedral : 24.189 164.350 3320 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.03 % Allowed : 7.84 % Favored : 91.14 % 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: 0.76 (0.23), residues: 1280 helix: 1.34 (0.18), residues: 788 sheet: -2.08 (0.57), residues: 68 loop : -0.52 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 52 HIS 0.004 0.001 HIS G 289 PHE 0.013 0.002 PHE B 265 TYR 0.009 0.001 TYR H 77 ARG 0.003 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 5 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 96 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.618 Fit side-chains REVERT: G 28 MET cc_start: 0.8625 (mmm) cc_final: 0.8364 (mmp) outliers start: 11 outliers final: 6 residues processed: 92 average time/residue: 0.4754 time to fit residues: 66.9357 Evaluate side-chains 87 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14208 Z= 0.196 Angle : 0.557 6.564 19904 Z= 0.335 Chirality : 0.036 0.128 2216 Planarity : 0.003 0.030 1984 Dihedral : 24.082 163.153 3320 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.84 % Allowed : 8.68 % Favored : 90.49 % 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: 1.14 (0.24), residues: 1280 helix: 1.63 (0.19), residues: 792 sheet: -1.99 (0.58), residues: 68 loop : -0.37 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 52 HIS 0.003 0.001 HIS A 99 PHE 0.010 0.001 PHE B 265 TYR 0.007 0.001 TYR H 77 ARG 0.002 0.000 ARG G 154 *********************** REFINEMENT MACRO_CYCLE 6 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 91 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 1.511 Fit side-chains REVERT: B 121 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7857 (ttt90) REVERT: G 28 MET cc_start: 0.8608 (mmm) cc_final: 0.8337 (mmp) outliers start: 9 outliers final: 5 residues processed: 88 average time/residue: 0.5275 time to fit residues: 69.6470 Evaluate side-chains 89 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 86 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14208 Z= 0.290 Angle : 0.585 6.954 19904 Z= 0.352 Chirality : 0.039 0.134 2216 Planarity : 0.004 0.032 1984 Dihedral : 24.156 164.453 3320 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.75 % Allowed : 9.61 % Favored : 89.65 % 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: 0.97 (0.24), residues: 1280 helix: 1.55 (0.19), residues: 790 sheet: -2.01 (0.58), residues: 68 loop : -0.56 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 52 HIS 0.003 0.001 HIS G 289 PHE 0.012 0.001 PHE B 64 TYR 0.010 0.001 TYR H 77 ARG 0.002 0.000 ARG H 297 *********************** REFINEMENT MACRO_CYCLE 7 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 90 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.937 Fit side-chains revert: symmetry clash REVERT: B 121 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7923 (ttt90) REVERT: G 28 MET cc_start: 0.8606 (mmm) cc_final: 0.8334 (mmp) outliers start: 8 outliers final: 7 residues processed: 88 average time/residue: 0.5441 time to fit residues: 71.7135 Evaluate side-chains 88 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 245 ASN Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14208 Z= 0.288 Angle : 0.589 6.815 19904 Z= 0.354 Chirality : 0.039 0.136 2216 Planarity : 0.004 0.032 1984 Dihedral : 24.232 163.988 3320 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.93 % Allowed : 9.79 % Favored : 89.27 % 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: 0.88 (0.24), residues: 1280 helix: 1.50 (0.18), residues: 790 sheet: -2.00 (0.57), residues: 68 loop : -0.65 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 52 HIS 0.003 0.001 HIS G 289 PHE 0.013 0.001 PHE B 265 TYR 0.010 0.001 TYR H 77 ARG 0.002 0.000 ARG H 297 *********************** REFINEMENT MACRO_CYCLE 8 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 90 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 2.085 Fit side-chains REVERT: B 121 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7901 (ttt90) REVERT: G 28 MET cc_start: 0.8614 (mmm) cc_final: 0.8338 (mmp) outliers start: 10 outliers final: 8 residues processed: 88 average time/residue: 0.5112 time to fit residues: 67.6324 Evaluate side-chains 89 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14208 Z= 0.190 Angle : 0.546 6.452 19904 Z= 0.328 Chirality : 0.036 0.129 2216 Planarity : 0.003 0.029 1984 Dihedral : 24.121 163.809 3320 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.93 % Allowed : 9.98 % Favored : 89.09 % 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: 1.24 (0.24), residues: 1280 helix: 1.77 (0.19), residues: 794 sheet: -1.87 (0.58), residues: 68 loop : -0.48 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 52 HIS 0.003 0.001 HIS G 289 PHE 0.009 0.001 PHE B 265 TYR 0.007 0.001 TYR H 77 ARG 0.002 0.000 ARG G 154 *********************** REFINEMENT MACRO_CYCLE 9 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 93 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.769 Fit side-chains REVERT: B 121 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7841 (ttt90) REVERT: G 28 MET cc_start: 0.8609 (mmm) cc_final: 0.8329 (mmp) outliers start: 10 outliers final: 8 residues processed: 91 average time/residue: 0.5062 time to fit residues: 69.0994 Evaluate side-chains 91 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 143 optimal weight: 0.0970 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14208 Z= 0.270 Angle : 0.574 7.180 19904 Z= 0.343 Chirality : 0.039 0.134 2216 Planarity : 0.004 0.031 1984 Dihedral : 24.192 164.663 3320 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.93 % Allowed : 10.07 % Favored : 88.99 % 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: 1.09 (0.24), residues: 1280 helix: 1.68 (0.19), residues: 792 sheet: -1.94 (0.58), residues: 68 loop : -0.61 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 52 HIS 0.003 0.001 HIS A 99 PHE 0.011 0.001 PHE B 64 TYR 0.010 0.001 TYR H 77 ARG 0.003 0.000 ARG H 297 ********************** REFINEMENT MACRO_CYCLE 10 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 91 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 2.048 Fit side-chains REVERT: B 121 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7890 (ttt90) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.5261 time to fit residues: 70.3520 Evaluate side-chains 90 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 289 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.086703 restraints weight = 64043.822| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.15 r_work: 0.3014 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14208 Z= 0.199 Angle : 0.550 6.984 19904 Z= 0.329 Chirality : 0.036 0.130 2216 Planarity : 0.003 0.029 1984 Dihedral : 24.131 164.050 3320 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.93 % Allowed : 10.17 % Favored : 88.90 % 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: 1.27 (0.24), residues: 1280 helix: 1.82 (0.19), residues: 794 sheet: -1.84 (0.58), residues: 68 loop : -0.54 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 52 HIS 0.003 0.001 HIS G 289 PHE 0.009 0.001 PHE B 265 TYR 0.007 0.001 TYR H 77 ARG 0.001 0.000 ARG H 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5204.47 seconds wall clock time: 92 minutes 37.57 seconds (5557.57 seconds total)