Starting phenix.real_space_refine on Sat Apr 6 22:17:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jir_36325/04_2024/8jir_36325_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jir_36325/04_2024/8jir_36325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jir_36325/04_2024/8jir_36325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jir_36325/04_2024/8jir_36325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jir_36325/04_2024/8jir_36325_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jir_36325/04_2024/8jir_36325_updated.pdb" } resolution = 2.57 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5731 2.51 5 N 1556 2.21 5 O 1671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R ARG 43": "NH1" <-> "NH2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "R ARG 227": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R GLU 408": "OE1" <-> "OE2" Residue "R GLU 412": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9014 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1884 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2581 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2886 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 13, 'TRANS': 369} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 4, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 206 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.86, per 1000 atoms: 0.65 Number of scatterers: 9014 At special positions: 0 Unit cell: (80.325, 100.674, 175.644, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1671 8.00 N 1556 7.00 C 5731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.87 Conformation dependent library (CDL) restraints added in 1.8 seconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 12 sheets defined 35.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.932A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.658A pdb=" N ASP A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 299 through 318 removed outlier: 3.682A pdb=" N TYR A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 357 removed outlier: 3.550A pdb=" N ASP A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 23 Processing helix chain 'B' and resid 2 through 22 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 45 Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'R' and resid 32 through 52 Processing helix chain 'R' and resid 90 through 93 No H-bonds generated for 'chain 'R' and resid 90 through 93' Processing helix chain 'R' and resid 139 through 168 removed outlier: 3.531A pdb=" N ALA R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 199 Processing helix chain 'R' and resid 208 through 214 Processing helix chain 'R' and resid 224 through 256 removed outlier: 3.591A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU R 247 " --> pdb=" O TRP R 243 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 291 Proline residue: R 277 - end of helix removed outlier: 3.938A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 304 through 306 No H-bonds generated for 'chain 'R' and resid 304 through 306' Processing helix chain 'R' and resid 311 through 337 Processing helix chain 'R' and resid 345 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 365 Processing helix chain 'R' and resid 378 through 403 removed outlier: 4.239A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 420 removed outlier: 3.569A pdb=" N PHE R 413 " --> pdb=" O VAL R 409 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 326 through 329 removed outlier: 7.098A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN A 195 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU A 36 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N HIS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU A 38 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N VAL A 201 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.949A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.714A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.535A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 207 through 212 removed outlier: 4.312A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.909A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.628A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.070A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 315 through 320 removed outlier: 7.002A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.530A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'R' and resid 80 through 82 382 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1526 1.32 - 1.45: 2718 1.45 - 1.58: 4881 1.58 - 1.72: 0 1.72 - 1.85: 76 Bond restraints: 9201 Sorted by residual: bond pdb=" CA ARG B 150 " pdb=" C ARG B 150 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.04e-02 9.25e+03 3.20e+01 bond pdb=" CA GLY B 244 " pdb=" C GLY B 244 " ideal model delta sigma weight residual 1.520 1.480 0.041 7.30e-03 1.88e+04 3.09e+01 bond pdb=" CA TYR N 32 " pdb=" C TYR N 32 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.21e-02 6.83e+03 2.40e+01 bond pdb=" C ARG B 150 " pdb=" O ARG B 150 " ideal model delta sigma weight residual 1.234 1.183 0.051 1.07e-02 8.73e+03 2.30e+01 bond pdb=" CA ILE B 58 " pdb=" C ILE B 58 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.19e-02 7.06e+03 1.33e+01 ... (remaining 9196 not shown) Histogram of bond angle deviations from ideal: 96.71 - 104.35: 109 104.35 - 111.98: 4490 111.98 - 119.61: 3220 119.61 - 127.25: 4560 127.25 - 134.88: 100 Bond angle restraints: 12479 Sorted by residual: angle pdb=" N GLY A 183 " pdb=" CA GLY A 183 " pdb=" C GLY A 183 " ideal model delta sigma weight residual 111.67 120.86 -9.19 9.20e-01 1.18e+00 9.97e+01 angle pdb=" N ASP R 122 " pdb=" CA ASP R 122 " pdb=" C ASP R 122 " ideal model delta sigma weight residual 113.19 101.88 11.31 1.19e+00 7.06e-01 9.04e+01 angle pdb=" N GLU R 125 " pdb=" CA GLU R 125 " pdb=" C GLU R 125 " ideal model delta sigma weight residual 109.62 96.71 12.91 1.50e+00 4.44e-01 7.40e+01 angle pdb=" N LEU R 32 " pdb=" CA LEU R 32 " pdb=" C LEU R 32 " ideal model delta sigma weight residual 111.14 103.47 7.67 1.08e+00 8.57e-01 5.04e+01 angle pdb=" N LEU B 152 " pdb=" CA LEU B 152 " pdb=" C LEU B 152 " ideal model delta sigma weight residual 111.14 104.00 7.14 1.08e+00 8.57e-01 4.38e+01 ... (remaining 12474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4875 17.97 - 35.94: 410 35.94 - 53.90: 127 53.90 - 71.87: 26 71.87 - 89.84: 17 Dihedral angle restraints: 5455 sinusoidal: 2055 harmonic: 3400 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual 93.00 -177.16 -89.84 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 154.60 -61.60 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 151.41 -58.41 1 1.00e+01 1.00e-02 4.57e+01 ... (remaining 5452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1272 0.099 - 0.197: 111 0.197 - 0.296: 19 0.296 - 0.395: 2 0.395 - 0.494: 2 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA ASN B 155 " pdb=" N ASN B 155 " pdb=" C ASN B 155 " pdb=" CB ASN B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.09e+00 chirality pdb=" CA HIS B 142 " pdb=" N HIS B 142 " pdb=" C HIS B 142 " pdb=" CB HIS B 142 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CA ILE B 37 " pdb=" N ILE B 37 " pdb=" C ILE B 37 " pdb=" CB ILE B 37 " both_signs ideal model delta sigma weight residual False 2.43 2.05 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 1403 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 101 " -0.045 2.00e-02 2.50e+03 7.63e-02 7.28e+01 pdb=" C04 D6M P 101 " 0.092 2.00e-02 2.50e+03 pdb=" C12 D6M P 101 " 0.075 2.00e-02 2.50e+03 pdb=" N03 D6M P 101 " -0.114 2.00e-02 2.50e+03 pdb=" O01 D6M P 101 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 205 " -0.023 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C TYR R 205 " 0.081 2.00e-02 2.50e+03 pdb=" O TYR R 205 " -0.031 2.00e-02 2.50e+03 pdb=" N SER R 206 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 57 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C LYS B 57 " -0.064 2.00e-02 2.50e+03 pdb=" O LYS B 57 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE B 58 " 0.021 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 73 2.56 - 3.14: 7578 3.14 - 3.73: 14071 3.73 - 4.31: 19854 4.31 - 4.90: 32547 Nonbonded interactions: 74123 Sorted by model distance: nonbonded pdb=" OE1 GLU P 15 " pdb=" OH TYR R 205 " model vdw 1.972 2.440 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.186 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.206 2.440 nonbonded pdb=" OG1 THR N 28 " pdb=" CE1 TYR N 32 " model vdw 2.221 3.340 nonbonded pdb=" NH2 ARG A 205 " pdb=" OD1 ASP B 186 " model vdw 2.221 2.520 ... (remaining 74118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.120 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 31.730 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:16.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.010 0.059 9201 Z= 0.649 Angle : 1.023 12.907 12479 Z= 0.643 Chirality : 0.065 0.494 1406 Planarity : 0.006 0.083 1590 Dihedral : 15.934 87.516 3240 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.95 % Favored : 92.53 % Rotamer: Outliers : 6.61 % Allowed : 3.47 % Favored : 89.92 % Cbeta Deviations : 0.27 % 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: -1.76 (0.24), residues: 1151 helix: 0.14 (0.25), residues: 434 sheet: -1.47 (0.32), residues: 236 loop : -2.20 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 248 HIS 0.012 0.002 HIS B 225 PHE 0.024 0.002 PHE B 151 TYR 0.033 0.003 TYR N 117 ARG 0.004 0.001 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 168 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: A 226 ASP cc_start: 0.8592 (t0) cc_final: 0.8311 (t0) REVERT: A 266 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8526 (mp0) REVERT: A 274 LYS cc_start: 0.8918 (pptt) cc_final: 0.8677 (pptt) REVERT: P 27 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.9005 (mmtt) REVERT: B 260 GLU cc_start: 0.8215 (pt0) cc_final: 0.7754 (pm20) REVERT: B 280 LYS cc_start: 0.8841 (tmtt) cc_final: 0.8537 (tmtt) REVERT: B 338 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8537 (mm) REVERT: G 36 ASP cc_start: 0.8284 (m-30) cc_final: 0.7992 (m-30) REVERT: N 117 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: N 123 GLN cc_start: 0.8262 (tp-100) cc_final: 0.8030 (tm-30) REVERT: N 124 VAL cc_start: 0.7635 (OUTLIER) cc_final: 0.7097 (p) REVERT: N 125 THR cc_start: 0.8974 (m) cc_final: 0.8413 (m) REVERT: R 222 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8321 (p0) outliers start: 61 outliers final: 13 residues processed: 205 average time/residue: 1.2967 time to fit residues: 282.4426 Evaluate side-chains 146 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 14 LYS Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 197 LYS Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN R 140 GLN R 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9201 Z= 0.230 Angle : 0.610 9.060 12479 Z= 0.325 Chirality : 0.043 0.230 1406 Planarity : 0.005 0.060 1590 Dihedral : 8.880 89.894 1322 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.08 % Favored : 95.66 % Rotamer: Outliers : 3.47 % Allowed : 14.41 % Favored : 82.12 % 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: -0.73 (0.25), residues: 1151 helix: 1.41 (0.25), residues: 435 sheet: -1.47 (0.32), residues: 229 loop : -1.74 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 306 HIS 0.006 0.001 HIS R 173 PHE 0.012 0.001 PHE B 151 TYR 0.024 0.002 TYR N 60 ARG 0.006 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 1.097 Fit side-chains REVERT: A 235 GLU cc_start: 0.8438 (tp30) cc_final: 0.8084 (tp30) REVERT: A 266 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8447 (mp0) REVERT: A 274 LYS cc_start: 0.8952 (pptt) cc_final: 0.8711 (pptt) REVERT: P 27 LYS cc_start: 0.9178 (mtmm) cc_final: 0.8816 (mmtt) REVERT: B 215 GLU cc_start: 0.8474 (pm20) cc_final: 0.7722 (pm20) REVERT: B 260 GLU cc_start: 0.8151 (pt0) cc_final: 0.7725 (pm20) REVERT: B 268 ASN cc_start: 0.8671 (m110) cc_final: 0.8464 (m110) REVERT: N 117 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: N 124 VAL cc_start: 0.6876 (OUTLIER) cc_final: 0.6551 (p) REVERT: N 125 THR cc_start: 0.8880 (m) cc_final: 0.8262 (m) REVERT: R 265 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7954 (tp) outliers start: 32 outliers final: 14 residues processed: 163 average time/residue: 1.2438 time to fit residues: 216.2037 Evaluate side-chains 158 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain R residue 409 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 82 optimal weight: 50.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN G 11 GLN R 140 GLN ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9201 Z= 0.186 Angle : 0.542 7.116 12479 Z= 0.287 Chirality : 0.041 0.148 1406 Planarity : 0.004 0.054 1590 Dihedral : 7.955 89.546 1297 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 2.71 % Allowed : 18.09 % Favored : 79.20 % 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: -0.32 (0.25), residues: 1151 helix: 1.84 (0.26), residues: 432 sheet: -1.26 (0.32), residues: 229 loop : -1.58 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 120 HIS 0.004 0.001 HIS R 173 PHE 0.011 0.001 PHE B 151 TYR 0.020 0.001 TYR R 148 ARG 0.005 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 1.042 Fit side-chains REVERT: A 206 ASP cc_start: 0.8455 (t0) cc_final: 0.8132 (t0) REVERT: A 226 ASP cc_start: 0.8054 (t0) cc_final: 0.7780 (t0) REVERT: A 235 GLU cc_start: 0.8382 (tp30) cc_final: 0.7775 (tp30) REVERT: A 266 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8345 (mp0) REVERT: P 27 LYS cc_start: 0.9238 (mtmm) cc_final: 0.8808 (mmtt) REVERT: B 260 GLU cc_start: 0.8168 (pt0) cc_final: 0.7698 (pm20) REVERT: B 268 ASN cc_start: 0.8657 (m110) cc_final: 0.8443 (m110) REVERT: B 325 MET cc_start: 0.8354 (mmt) cc_final: 0.8151 (tpp) REVERT: R 265 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7943 (tp) REVERT: R 308 ILE cc_start: 0.8817 (pt) cc_final: 0.8612 (pp) REVERT: R 338 ASN cc_start: 0.7440 (t0) cc_final: 0.6493 (t0) REVERT: R 408 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7901 (mp0) REVERT: R 409 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8286 (p) outliers start: 25 outliers final: 14 residues processed: 167 average time/residue: 1.2294 time to fit residues: 219.8281 Evaluate side-chains 160 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 214 TRP Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain R residue 409 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9201 Z= 0.191 Angle : 0.552 8.050 12479 Z= 0.291 Chirality : 0.041 0.196 1406 Planarity : 0.004 0.045 1590 Dihedral : 7.549 89.143 1292 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 2.93 % Allowed : 20.91 % Favored : 76.16 % 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: -0.13 (0.25), residues: 1151 helix: 1.99 (0.26), residues: 439 sheet: -1.13 (0.32), residues: 231 loop : -1.55 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 120 HIS 0.004 0.001 HIS A 324 PHE 0.010 0.001 PHE R 324 TYR 0.020 0.001 TYR R 148 ARG 0.006 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 0.994 Fit side-chains REVERT: A 206 ASP cc_start: 0.8462 (t0) cc_final: 0.8136 (t0) REVERT: A 226 ASP cc_start: 0.8083 (t0) cc_final: 0.7860 (t0) REVERT: A 235 GLU cc_start: 0.8228 (tp30) cc_final: 0.7868 (tp30) REVERT: A 266 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8347 (mp0) REVERT: P 20 GLN cc_start: 0.8663 (tp40) cc_final: 0.8433 (mm-40) REVERT: B 61 MET cc_start: 0.9131 (pp-130) cc_final: 0.8447 (pp-130) REVERT: B 217 MET cc_start: 0.7931 (pmt) cc_final: 0.7685 (pmm) REVERT: B 260 GLU cc_start: 0.8141 (pt0) cc_final: 0.7632 (pm20) REVERT: B 268 ASN cc_start: 0.8625 (m110) cc_final: 0.8411 (m110) REVERT: B 280 LYS cc_start: 0.8685 (tptp) cc_final: 0.7987 (tmtt) REVERT: B 296 VAL cc_start: 0.8905 (t) cc_final: 0.8664 (m) REVERT: G 32 LYS cc_start: 0.8086 (ttpp) cc_final: 0.7882 (tppp) REVERT: R 202 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8039 (ptpp) REVERT: R 265 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7930 (tp) REVERT: R 408 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7924 (mp0) outliers start: 27 outliers final: 13 residues processed: 160 average time/residue: 1.2373 time to fit residues: 211.4203 Evaluate side-chains 150 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 214 TRP Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.0070 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 190 GLN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9201 Z= 0.172 Angle : 0.527 6.567 12479 Z= 0.280 Chirality : 0.040 0.157 1406 Planarity : 0.004 0.041 1590 Dihedral : 7.309 86.567 1290 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.36 % Allowed : 21.89 % Favored : 74.76 % 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: 0.10 (0.25), residues: 1151 helix: 2.17 (0.26), residues: 438 sheet: -0.97 (0.33), residues: 218 loop : -1.42 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 214 HIS 0.003 0.001 HIS A 324 PHE 0.010 0.001 PHE R 324 TYR 0.019 0.001 TYR R 148 ARG 0.005 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.113 Fit side-chains REVERT: A 190 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8689 (tt0) REVERT: A 200 ASP cc_start: 0.7688 (t0) cc_final: 0.7379 (t0) REVERT: A 201 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8968 (t) REVERT: A 206 ASP cc_start: 0.8459 (t0) cc_final: 0.8145 (t0) REVERT: A 226 ASP cc_start: 0.8046 (t0) cc_final: 0.7841 (t0) REVERT: A 235 GLU cc_start: 0.8320 (tp30) cc_final: 0.7802 (tp30) REVERT: A 259 ASN cc_start: 0.8723 (t0) cc_final: 0.8452 (t160) REVERT: A 266 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8300 (mp0) REVERT: P 20 GLN cc_start: 0.8661 (tp40) cc_final: 0.8428 (mm-40) REVERT: B 61 MET cc_start: 0.9144 (pp-130) cc_final: 0.8565 (pp-130) REVERT: B 215 GLU cc_start: 0.8527 (pm20) cc_final: 0.8107 (pm20) REVERT: B 217 MET cc_start: 0.7892 (pmt) cc_final: 0.7562 (pmt) REVERT: B 260 GLU cc_start: 0.8094 (pt0) cc_final: 0.7578 (pm20) REVERT: B 268 ASN cc_start: 0.8543 (m110) cc_final: 0.8145 (p0) REVERT: B 280 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8336 (tttp) REVERT: G 42 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7884 (mp0) REVERT: N 87 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7543 (ttmt) REVERT: R 265 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7927 (tp) REVERT: R 408 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7905 (mp0) outliers start: 31 outliers final: 14 residues processed: 163 average time/residue: 1.2077 time to fit residues: 210.7500 Evaluate side-chains 153 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 109 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 190 GLN P 13 GLN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9201 Z= 0.183 Angle : 0.546 7.627 12479 Z= 0.289 Chirality : 0.040 0.147 1406 Planarity : 0.004 0.040 1590 Dihedral : 7.192 84.788 1290 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.82 % Allowed : 22.75 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1151 helix: 2.21 (0.26), residues: 439 sheet: -0.81 (0.33), residues: 215 loop : -1.41 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 243 HIS 0.003 0.001 HIS A 324 PHE 0.010 0.001 PHE R 324 TYR 0.018 0.001 TYR R 148 ARG 0.006 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.056 Fit side-chains REVERT: A 190 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8704 (tt0) REVERT: A 200 ASP cc_start: 0.7672 (t0) cc_final: 0.7367 (t0) REVERT: A 201 VAL cc_start: 0.9215 (OUTLIER) cc_final: 0.8972 (t) REVERT: A 206 ASP cc_start: 0.8465 (t0) cc_final: 0.8143 (t0) REVERT: A 226 ASP cc_start: 0.8037 (t0) cc_final: 0.7835 (t0) REVERT: A 235 GLU cc_start: 0.8289 (tp30) cc_final: 0.7768 (tp30) REVERT: P 20 GLN cc_start: 0.8641 (tp40) cc_final: 0.8378 (mm-40) REVERT: B 61 MET cc_start: 0.9124 (pp-130) cc_final: 0.8586 (pp-130) REVERT: B 215 GLU cc_start: 0.8426 (pm20) cc_final: 0.8131 (pm20) REVERT: B 260 GLU cc_start: 0.8099 (pt0) cc_final: 0.7579 (pm20) REVERT: B 268 ASN cc_start: 0.8544 (m110) cc_final: 0.8162 (p0) REVERT: B 280 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8339 (tttp) REVERT: G 42 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7906 (mp0) REVERT: N 87 LYS cc_start: 0.7812 (ttmm) cc_final: 0.7568 (ttmt) REVERT: R 204 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.5641 (pmt) REVERT: R 221 GLN cc_start: 0.8015 (mt0) cc_final: 0.7718 (mm-40) REVERT: R 265 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7930 (tp) REVERT: R 408 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7913 (mp0) outliers start: 26 outliers final: 14 residues processed: 155 average time/residue: 1.2248 time to fit residues: 202.8272 Evaluate side-chains 155 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 40.0000 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.0060 chunk 43 optimal weight: 1.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 190 GLN A 259 ASN B 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9201 Z= 0.206 Angle : 0.545 8.111 12479 Z= 0.288 Chirality : 0.041 0.162 1406 Planarity : 0.004 0.039 1590 Dihedral : 6.976 83.031 1288 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.82 % Allowed : 23.40 % Favored : 73.78 % 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: 0.26 (0.25), residues: 1151 helix: 2.25 (0.26), residues: 439 sheet: -0.73 (0.33), residues: 215 loop : -1.36 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 243 HIS 0.003 0.001 HIS A 324 PHE 0.010 0.001 PHE R 324 TYR 0.018 0.001 TYR R 148 ARG 0.006 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 0.974 Fit side-chains REVERT: A 190 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8651 (tt0) REVERT: A 200 ASP cc_start: 0.7665 (t0) cc_final: 0.7368 (t0) REVERT: A 201 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8976 (t) REVERT: A 206 ASP cc_start: 0.8473 (t0) cc_final: 0.8151 (t0) REVERT: A 226 ASP cc_start: 0.8168 (t0) cc_final: 0.7952 (t0) REVERT: A 235 GLU cc_start: 0.8300 (tp30) cc_final: 0.7764 (tp30) REVERT: P 20 GLN cc_start: 0.8662 (tp40) cc_final: 0.8408 (mm-40) REVERT: B 61 MET cc_start: 0.9145 (pp-130) cc_final: 0.8656 (pp-130) REVERT: B 217 MET cc_start: 0.8140 (pmt) cc_final: 0.7826 (pmm) REVERT: B 260 GLU cc_start: 0.8112 (pt0) cc_final: 0.7625 (pm20) REVERT: B 268 ASN cc_start: 0.8546 (m110) cc_final: 0.8235 (p0) REVERT: B 280 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8335 (tttp) REVERT: G 42 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7921 (mp0) REVERT: R 204 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.5734 (pmt) REVERT: R 221 GLN cc_start: 0.7984 (mt0) cc_final: 0.7666 (mm-40) REVERT: R 265 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7920 (tp) outliers start: 26 outliers final: 15 residues processed: 157 average time/residue: 1.1911 time to fit residues: 199.6804 Evaluate side-chains 152 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 190 GLN B 32 GLN R 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9201 Z= 0.178 Angle : 0.555 10.165 12479 Z= 0.290 Chirality : 0.040 0.149 1406 Planarity : 0.004 0.039 1590 Dihedral : 6.800 80.417 1288 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.71 % Allowed : 24.05 % Favored : 73.24 % 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: 0.36 (0.25), residues: 1151 helix: 2.31 (0.26), residues: 439 sheet: -0.60 (0.33), residues: 213 loop : -1.30 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 243 HIS 0.003 0.001 HIS A 324 PHE 0.010 0.001 PHE R 324 TYR 0.017 0.001 TYR R 148 ARG 0.006 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.059 Fit side-chains REVERT: A 190 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8614 (tt0) REVERT: A 200 ASP cc_start: 0.7641 (t0) cc_final: 0.7358 (OUTLIER) REVERT: A 201 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8948 (t) REVERT: A 206 ASP cc_start: 0.8458 (t0) cc_final: 0.8132 (t0) REVERT: A 226 ASP cc_start: 0.8153 (t0) cc_final: 0.7933 (t0) REVERT: A 235 GLU cc_start: 0.8330 (tp30) cc_final: 0.7768 (tp30) REVERT: A 274 LYS cc_start: 0.9110 (pptt) cc_final: 0.8801 (pptt) REVERT: B 217 MET cc_start: 0.8282 (pmt) cc_final: 0.7932 (pmm) REVERT: B 260 GLU cc_start: 0.8080 (pt0) cc_final: 0.7591 (pm20) REVERT: B 268 ASN cc_start: 0.8537 (m110) cc_final: 0.8226 (p0) REVERT: B 280 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8329 (tttp) REVERT: G 42 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7934 (mp0) REVERT: N 38 ARG cc_start: 0.8581 (ptt-90) cc_final: 0.8171 (ptm-80) REVERT: N 89 GLU cc_start: 0.8359 (mp0) cc_final: 0.8154 (pp20) REVERT: R 265 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7926 (tp) REVERT: R 338 ASN cc_start: 0.7245 (t0) cc_final: 0.6993 (OUTLIER) REVERT: R 408 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7882 (mp0) outliers start: 25 outliers final: 17 residues processed: 151 average time/residue: 1.3621 time to fit residues: 219.1605 Evaluate side-chains 152 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 30.0000 chunk 31 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 190 GLN B 32 GLN R 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9201 Z= 0.201 Angle : 0.566 9.405 12479 Z= 0.297 Chirality : 0.041 0.157 1406 Planarity : 0.004 0.039 1590 Dihedral : 6.532 77.732 1286 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.49 % Allowed : 24.49 % Favored : 73.02 % 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: 0.39 (0.25), residues: 1151 helix: 2.32 (0.26), residues: 439 sheet: -0.59 (0.33), residues: 215 loop : -1.27 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 243 HIS 0.003 0.001 HIS A 324 PHE 0.010 0.001 PHE R 324 TYR 0.018 0.001 TYR R 148 ARG 0.007 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.116 Fit side-chains REVERT: A 190 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8659 (tt0) REVERT: A 200 ASP cc_start: 0.7689 (t0) cc_final: 0.7389 (OUTLIER) REVERT: A 201 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8958 (t) REVERT: A 206 ASP cc_start: 0.8461 (t0) cc_final: 0.8136 (t0) REVERT: A 226 ASP cc_start: 0.8173 (t0) cc_final: 0.7958 (t0) REVERT: A 235 GLU cc_start: 0.8339 (tp30) cc_final: 0.7586 (tp30) REVERT: A 274 LYS cc_start: 0.9091 (pptt) cc_final: 0.8775 (pptt) REVERT: B 215 GLU cc_start: 0.8373 (pm20) cc_final: 0.8142 (pm20) REVERT: B 217 MET cc_start: 0.8272 (pmt) cc_final: 0.7978 (pmm) REVERT: B 260 GLU cc_start: 0.8113 (pt0) cc_final: 0.7618 (pm20) REVERT: B 268 ASN cc_start: 0.8543 (m110) cc_final: 0.8227 (p0) REVERT: B 280 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8231 (tttp) REVERT: G 42 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7933 (mp0) REVERT: N 38 ARG cc_start: 0.8590 (ptt-90) cc_final: 0.8174 (ptm-80) REVERT: N 89 GLU cc_start: 0.8424 (mp0) cc_final: 0.8029 (pp20) REVERT: N 106 ASP cc_start: 0.8364 (p0) cc_final: 0.8035 (p0) REVERT: R 204 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.5902 (pmt) REVERT: R 221 GLN cc_start: 0.7974 (mt0) cc_final: 0.7654 (mm-40) REVERT: R 265 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7929 (tp) REVERT: R 408 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7889 (mp0) outliers start: 23 outliers final: 13 residues processed: 155 average time/residue: 1.2754 time to fit residues: 210.5047 Evaluate side-chains 155 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 0.3980 chunk 54 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 190 GLN B 32 GLN R 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9201 Z= 0.178 Angle : 0.568 9.615 12479 Z= 0.295 Chirality : 0.040 0.152 1406 Planarity : 0.004 0.039 1590 Dihedral : 6.348 74.019 1286 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.28 % Allowed : 24.81 % Favored : 72.91 % 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: 0.44 (0.25), residues: 1151 helix: 2.32 (0.26), residues: 441 sheet: -0.54 (0.33), residues: 212 loop : -1.23 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 243 HIS 0.003 0.001 HIS A 324 PHE 0.011 0.001 PHE A 189 TYR 0.017 0.001 TYR R 148 ARG 0.007 0.000 ARG A 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 142 time to evaluate : 1.126 Fit side-chains REVERT: A 190 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8634 (tt0) REVERT: A 200 ASP cc_start: 0.7651 (t0) cc_final: 0.7353 (OUTLIER) REVERT: A 201 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8951 (t) REVERT: A 206 ASP cc_start: 0.8445 (t0) cc_final: 0.8116 (t0) REVERT: A 226 ASP cc_start: 0.8198 (t0) cc_final: 0.7960 (t0) REVERT: A 235 GLU cc_start: 0.8339 (tp30) cc_final: 0.7765 (tp30) REVERT: A 274 LYS cc_start: 0.9064 (pptt) cc_final: 0.8743 (pptt) REVERT: B 17 GLN cc_start: 0.8253 (tm-30) cc_final: 0.8038 (tm-30) REVERT: B 61 MET cc_start: 0.9107 (pp-130) cc_final: 0.8269 (pp-130) REVERT: B 215 GLU cc_start: 0.8454 (pm20) cc_final: 0.8226 (pm20) REVERT: B 217 MET cc_start: 0.8265 (pmt) cc_final: 0.7964 (pmm) REVERT: B 260 GLU cc_start: 0.8068 (pt0) cc_final: 0.7543 (pm20) REVERT: B 268 ASN cc_start: 0.8554 (m110) cc_final: 0.8215 (p0) REVERT: B 280 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8266 (tttp) REVERT: G 42 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7917 (mp0) REVERT: N 38 ARG cc_start: 0.8571 (ptt-90) cc_final: 0.8170 (ptm-80) REVERT: N 89 GLU cc_start: 0.8414 (mp0) cc_final: 0.8213 (pp20) REVERT: N 106 ASP cc_start: 0.8369 (p0) cc_final: 0.8044 (p0) REVERT: R 204 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.5907 (pmt) REVERT: R 221 GLN cc_start: 0.8005 (mt0) cc_final: 0.7721 (mt0) REVERT: R 265 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7919 (tp) REVERT: R 408 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7888 (mp0) outliers start: 21 outliers final: 12 residues processed: 155 average time/residue: 1.2932 time to fit residues: 213.6673 Evaluate side-chains 153 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 265 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0570 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 190 GLN P 13 GLN B 32 GLN R 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.080737 restraints weight = 15865.230| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.21 r_work: 0.2996 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9201 Z= 0.183 Angle : 0.575 13.082 12479 Z= 0.298 Chirality : 0.041 0.151 1406 Planarity : 0.004 0.038 1590 Dihedral : 6.130 69.375 1286 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.06 % Allowed : 25.03 % Favored : 72.91 % 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: 0.46 (0.25), residues: 1151 helix: 2.45 (0.26), residues: 435 sheet: -0.61 (0.33), residues: 214 loop : -1.25 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 243 HIS 0.003 0.001 HIS A 324 PHE 0.011 0.001 PHE A 189 TYR 0.017 0.001 TYR R 148 ARG 0.007 0.000 ARG A 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3972.01 seconds wall clock time: 71 minutes 46.41 seconds (4306.41 seconds total)