Starting phenix.real_space_refine on Tue Feb 13 23:31:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f55_31458/02_2024/7f55_31458_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f55_31458/02_2024/7f55_31458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f55_31458/02_2024/7f55_31458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f55_31458/02_2024/7f55_31458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f55_31458/02_2024/7f55_31458_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f55_31458/02_2024/7f55_31458_updated.pdb" } resolution = 3.1 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 62 5.16 5 C 5127 2.51 5 N 1397 2.21 5 O 1501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 392": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 122": "OD1" <-> "OD2" Residue "R PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 308": "OE1" <-> "OE2" Residue "R GLU 315": "OE1" <-> "OE2" Residue "L ARG 5": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8088 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1885 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2133 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain breaks: 2 Chain: "L" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 70 Classifications: {'peptide': 7} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'NLE:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 4.41, per 1000 atoms: 0.55 Number of scatterers: 8088 At special positions: 0 Unit cell: (86.19, 95.316, 122.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 62 16.00 O 1501 8.00 N 1397 7.00 C 5127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.04 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " 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=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.4 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN L 4 " Number of C-beta restraints generated: 1938 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 11 sheets defined 39.4% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.735A pdb=" N LYS A 17 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 27 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 28 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 38 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.837A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 390 removed outlier: 3.834A pdb=" N VAL A 375 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 377 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.913A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'G' and resid 7 through 23 removed outlier: 3.786A pdb=" N ARG G 13 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 48 through 70 Processing helix chain 'R' and resid 78 through 109 Processing helix chain 'R' and resid 117 through 152 removed outlier: 3.547A pdb=" N SER R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 160 No H-bonds generated for 'chain 'R' and resid 157 through 160' Processing helix chain 'R' and resid 163 through 186 Processing helix chain 'R' and resid 191 through 227 Processing helix chain 'R' and resid 239 through 270 removed outlier: 3.734A pdb=" N PHE R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 275 through 301 removed outlier: 3.621A pdb=" N CYS R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS R 283 " --> pdb=" O CYS R 279 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE R 284 " --> pdb=" O PHE R 280 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ASN R 285 " --> pdb=" O MET R 281 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU R 286 " --> pdb=" O SER R 282 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE R 289 " --> pdb=" O ASN R 285 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 307 through 319 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.465A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.814A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.095A 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: 7.010A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.177A 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: 6.668A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.863A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.657A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.451A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.443A 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 52 removed outlier: 6.909A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 18 through 20 removed outlier: 3.553A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.855A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1023 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: 2.17 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2467 1.34 - 1.46: 1922 1.46 - 1.58: 3763 1.58 - 1.71: 0 1.71 - 1.83: 87 Bond restraints: 8239 Sorted by residual: bond pdb=" C ASP A 274 " pdb=" O ASP A 274 " ideal model delta sigma weight residual 1.236 1.217 0.019 1.15e-02 7.56e+03 2.67e+00 bond pdb=" CG LYS L 7 " pdb=" CD LYS L 7 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.45e+00 bond pdb=" C TRP L 6 " pdb=" O TRP L 6 " ideal model delta sigma weight residual 1.233 1.213 0.021 1.43e-02 4.89e+03 2.12e+00 bond pdb=" C NLE L 1 " pdb=" O NLE L 1 " ideal model delta sigma weight residual 1.231 1.257 -0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C ASP R 122 " pdb=" O ASP R 122 " ideal model delta sigma weight residual 1.237 1.221 0.015 1.19e-02 7.06e+03 1.64e+00 ... (remaining 8234 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.37: 115 105.37 - 112.55: 4254 112.55 - 119.73: 2778 119.73 - 126.91: 3913 126.91 - 134.09: 89 Bond angle restraints: 11149 Sorted by residual: angle pdb=" CA DPN L 4 " pdb=" CB DPN L 4 " pdb=" CG DPN L 4 " ideal model delta sigma weight residual 113.80 105.91 7.89 1.00e+00 1.00e+00 6.23e+01 angle pdb=" N LEU R 286 " pdb=" CA LEU R 286 " pdb=" C LEU R 286 " ideal model delta sigma weight residual 113.41 107.55 5.86 1.22e+00 6.72e-01 2.31e+01 angle pdb=" CD LYS L 7 " pdb=" CE LYS L 7 " pdb=" NZ LYS L 7 " ideal model delta sigma weight residual 111.90 98.19 13.71 3.20e+00 9.77e-02 1.83e+01 angle pdb=" N HIS L 3 " pdb=" CA HIS L 3 " pdb=" C HIS L 3 " ideal model delta sigma weight residual 111.00 100.60 10.40 2.80e+00 1.28e-01 1.38e+01 angle pdb=" N VAL R 124 " pdb=" CA VAL R 124 " pdb=" C VAL R 124 " ideal model delta sigma weight residual 110.82 114.12 -3.30 9.70e-01 1.06e+00 1.16e+01 ... (remaining 11144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4635 17.58 - 35.16: 224 35.16 - 52.74: 45 52.74 - 70.32: 21 70.32 - 87.91: 4 Dihedral angle restraints: 4929 sinusoidal: 1939 harmonic: 2990 Sorted by residual: dihedral pdb=" CB CYS R 40 " pdb=" SG CYS R 40 " pdb=" SG CYS R 279 " pdb=" CB CYS R 279 " ideal model delta sinusoidal sigma weight residual -86.00 -35.53 -50.47 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CA TRP R 258 " pdb=" C TRP R 258 " pdb=" N ALA R 259 " pdb=" CA ALA R 259 " ideal model delta harmonic sigma weight residual -180.00 -156.53 -23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CB MET R 204 " pdb=" CG MET R 204 " pdb=" SD MET R 204 " pdb=" CE MET R 204 " ideal model delta sinusoidal sigma weight residual -180.00 -126.97 -53.03 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 4926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 901 0.048 - 0.096: 275 0.096 - 0.144: 80 0.144 - 0.192: 13 0.192 - 0.240: 5 Chirality restraints: 1274 Sorted by residual: chirality pdb=" CA GLU A 392 " pdb=" N GLU A 392 " pdb=" C GLU A 392 " pdb=" CB GLU A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA HIS R 283 " pdb=" N HIS R 283 " pdb=" C HIS R 283 " pdb=" CB HIS R 283 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ARG A 385 " pdb=" N ARG A 385 " pdb=" C ARG A 385 " pdb=" CB ARG A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.56e-01 ... (remaining 1271 not shown) Planarity restraints: 1415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 382 " 0.021 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C ILE A 382 " -0.071 2.00e-02 2.50e+03 pdb=" O ILE A 382 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE A 383 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 13 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ARG A 13 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG A 13 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN A 14 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 377 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C ASN A 377 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN A 377 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP A 378 " -0.021 2.00e-02 2.50e+03 ... (remaining 1412 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 3 1.98 - 2.71: 316 2.71 - 3.44: 11513 3.44 - 4.17: 19349 4.17 - 4.90: 35494 Nonbonded interactions: 66675 Sorted by model distance: nonbonded pdb=" CG ASP L 2 " pdb=" NZ LYS L 7 " model vdw 1.246 3.350 nonbonded pdb=" OD1 ASP L 2 " pdb=" NZ LYS L 7 " model vdw 1.674 2.520 nonbonded pdb=" CB ASP L 2 " pdb=" NZ LYS L 7 " model vdw 1.906 3.520 nonbonded pdb=" O ASP A 284 " pdb=" OD1 ASP A 284 " model vdw 2.132 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.216 2.440 ... (remaining 66670 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.930 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.630 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 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 0.047 8239 Z= 0.294 Angle : 0.902 13.706 11149 Z= 0.551 Chirality : 0.052 0.240 1274 Planarity : 0.007 0.041 1415 Dihedral : 11.819 87.906 2979 Min Nonbonded Distance : 1.246 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.90 % Favored : 98.00 % Rotamer: Outliers : 0.34 % Allowed : 2.49 % Favored : 97.18 % 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: 1.13 (0.26), residues: 1002 helix: 0.96 (0.23), residues: 411 sheet: 0.82 (0.34), residues: 224 loop : 0.70 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 99 HIS 0.008 0.002 HIS B 183 PHE 0.025 0.002 PHE B 199 TYR 0.016 0.002 TYR A 339 ARG 0.023 0.002 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 261 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8157 (mtmt) REVERT: A 218 ASN cc_start: 0.8357 (m-40) cc_final: 0.7774 (p0) REVERT: A 339 TYR cc_start: 0.7782 (m-80) cc_final: 0.7566 (m-80) REVERT: B 16 ASN cc_start: 0.6976 (m-40) cc_final: 0.6619 (t0) REVERT: B 37 ILE cc_start: 0.8693 (mm) cc_final: 0.8351 (pt) REVERT: B 111 TYR cc_start: 0.6769 (m-80) cc_final: 0.6294 (m-80) REVERT: B 146 LEU cc_start: 0.8304 (tp) cc_final: 0.7901 (mp) REVERT: B 217 MET cc_start: 0.6154 (ttt) cc_final: 0.5647 (mmm) REVERT: G 13 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7749 (ptt180) REVERT: G 21 MET cc_start: 0.8380 (mtm) cc_final: 0.8124 (ptp) REVERT: R 185 ILE cc_start: 0.8444 (mm) cc_final: 0.7867 (mm) REVERT: R 200 MET cc_start: 0.5703 (mtt) cc_final: 0.5180 (mtp) REVERT: R 258 TRP cc_start: 0.6863 (m100) cc_final: 0.6481 (m100) REVERT: R 316 ILE cc_start: 0.8349 (mt) cc_final: 0.7607 (mm) outliers start: 3 outliers final: 2 residues processed: 263 average time/residue: 0.2685 time to fit residues: 88.8608 Evaluate side-chains 170 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain L residue 7 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 59 GLN A 377 ASN A 390 GLN B 32 GLN B 88 ASN B 176 GLN G 44 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8239 Z= 0.374 Angle : 0.658 6.178 11149 Z= 0.370 Chirality : 0.047 0.152 1274 Planarity : 0.006 0.060 1415 Dihedral : 5.199 50.359 1122 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.18 % Allowed : 11.30 % Favored : 84.52 % 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: 1.23 (0.26), residues: 1002 helix: 1.42 (0.24), residues: 407 sheet: 0.69 (0.34), residues: 223 loop : 0.38 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 281 HIS 0.006 0.001 HIS B 54 PHE 0.029 0.003 PHE B 235 TYR 0.025 0.003 TYR R 157 ARG 0.008 0.001 ARG L 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 173 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7561 (mttt) cc_final: 0.7259 (mptt) REVERT: A 339 TYR cc_start: 0.7708 (m-80) cc_final: 0.7267 (m-80) REVERT: A 342 ARG cc_start: 0.7702 (ttp-170) cc_final: 0.7375 (ttt180) REVERT: A 347 ARG cc_start: 0.6786 (ptp-170) cc_final: 0.6534 (mtp-110) REVERT: A 370 GLU cc_start: 0.8369 (mp0) cc_final: 0.8036 (mp0) REVERT: B 16 ASN cc_start: 0.7247 (m-40) cc_final: 0.6833 (t0) REVERT: B 79 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8697 (tt) REVERT: B 146 LEU cc_start: 0.8748 (tp) cc_final: 0.8326 (mp) REVERT: B 234 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.8096 (m-80) REVERT: B 262 MET cc_start: 0.8533 (tpp) cc_final: 0.8219 (tpp) REVERT: B 325 MET cc_start: 0.7899 (mmt) cc_final: 0.7297 (mmt) REVERT: N 43 LYS cc_start: 0.7649 (mttt) cc_final: 0.7400 (mttt) REVERT: R 71 LYS cc_start: 0.6375 (mtmm) cc_final: 0.5960 (tttt) REVERT: R 204 MET cc_start: 0.5946 (mmm) cc_final: 0.5470 (mmt) REVERT: R 220 ARG cc_start: 0.6455 (mmt90) cc_final: 0.5969 (ttm-80) outliers start: 37 outliers final: 26 residues processed: 198 average time/residue: 0.2391 time to fit residues: 61.1386 Evaluate side-chains 181 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 309 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 24 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 267 GLN A 278 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8239 Z= 0.158 Angle : 0.490 5.573 11149 Z= 0.273 Chirality : 0.040 0.135 1274 Planarity : 0.004 0.046 1415 Dihedral : 4.433 49.061 1118 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.16 % Allowed : 14.35 % Favored : 82.49 % 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: 1.32 (0.26), residues: 1002 helix: 1.59 (0.25), residues: 407 sheet: 0.57 (0.33), residues: 233 loop : 0.42 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS R 264 PHE 0.021 0.001 PHE B 235 TYR 0.015 0.001 TYR R 187 ARG 0.004 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 0.913 Fit side-chains REVERT: A 24 LYS cc_start: 0.7781 (mttt) cc_final: 0.7487 (mptt) REVERT: A 347 ARG cc_start: 0.6604 (ptp-170) cc_final: 0.6400 (ptp90) REVERT: A 370 GLU cc_start: 0.8312 (mp0) cc_final: 0.7997 (mp0) REVERT: B 13 GLN cc_start: 0.8032 (tp40) cc_final: 0.7757 (mm-40) REVERT: B 16 ASN cc_start: 0.6929 (m-40) cc_final: 0.6645 (t0) REVERT: B 59 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.6117 (t80) REVERT: B 217 MET cc_start: 0.6437 (ttt) cc_final: 0.5941 (ptm) REVERT: B 234 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: B 262 MET cc_start: 0.8496 (tpp) cc_final: 0.8046 (tpp) REVERT: B 325 MET cc_start: 0.7911 (mmt) cc_final: 0.7513 (mmt) REVERT: G 22 GLU cc_start: 0.6331 (mt-10) cc_final: 0.6030 (mp0) REVERT: N 43 LYS cc_start: 0.7818 (mttt) cc_final: 0.7608 (mttt) REVERT: N 105 ARG cc_start: 0.8241 (ttp-170) cc_final: 0.7879 (ttp-110) REVERT: R 71 LYS cc_start: 0.6357 (mtmm) cc_final: 0.5923 (tttt) REVERT: R 204 MET cc_start: 0.5692 (mmm) cc_final: 0.5470 (mmt) REVERT: R 220 ARG cc_start: 0.6234 (mmt90) cc_final: 0.5746 (ttm-80) REVERT: R 241 MET cc_start: 0.5171 (ttp) cc_final: 0.4661 (ppp) outliers start: 28 outliers final: 22 residues processed: 193 average time/residue: 0.2402 time to fit residues: 60.1416 Evaluate side-chains 181 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 309 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 267 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8239 Z= 0.197 Angle : 0.504 5.437 11149 Z= 0.278 Chirality : 0.041 0.140 1274 Planarity : 0.004 0.042 1415 Dihedral : 4.355 49.481 1118 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.63 % Allowed : 14.24 % Favored : 81.13 % 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: 1.15 (0.26), residues: 1002 helix: 1.59 (0.25), residues: 407 sheet: 0.47 (0.33), residues: 226 loop : 0.16 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS R 264 PHE 0.017 0.002 PHE B 235 TYR 0.015 0.001 TYR R 187 ARG 0.005 0.000 ARG L 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 0.940 Fit side-chains REVERT: B 13 GLN cc_start: 0.8031 (tp40) cc_final: 0.7815 (mm-40) REVERT: B 16 ASN cc_start: 0.7053 (m-40) cc_final: 0.6747 (t0) REVERT: B 19 ARG cc_start: 0.6949 (mmt-90) cc_final: 0.6701 (mmt-90) REVERT: B 59 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.6315 (t80) REVERT: B 217 MET cc_start: 0.6520 (ttt) cc_final: 0.5986 (ptm) REVERT: B 234 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: B 262 MET cc_start: 0.8393 (tpp) cc_final: 0.8058 (tpp) REVERT: B 303 ASP cc_start: 0.7631 (m-30) cc_final: 0.7353 (m-30) REVERT: B 325 MET cc_start: 0.7879 (mmt) cc_final: 0.7414 (mmt) REVERT: G 22 GLU cc_start: 0.6353 (mt-10) cc_final: 0.6094 (mp0) REVERT: N 46 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7036 (mm-30) REVERT: R 71 LYS cc_start: 0.6047 (mtmm) cc_final: 0.5758 (tttt) REVERT: R 93 VAL cc_start: 0.4472 (OUTLIER) cc_final: 0.3990 (t) REVERT: R 150 THR cc_start: 0.8159 (p) cc_final: 0.7684 (m) REVERT: R 220 ARG cc_start: 0.6270 (mmt90) cc_final: 0.5754 (ttm-80) REVERT: R 314 LYS cc_start: 0.7200 (pttp) cc_final: 0.6570 (ptmt) outliers start: 41 outliers final: 31 residues processed: 185 average time/residue: 0.2309 time to fit residues: 55.6866 Evaluate side-chains 194 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 309 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 267 GLN A 292 ASN A 357 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8239 Z= 0.150 Angle : 0.481 6.009 11149 Z= 0.264 Chirality : 0.041 0.140 1274 Planarity : 0.004 0.043 1415 Dihedral : 4.227 49.846 1118 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.29 % Allowed : 15.93 % Favored : 79.77 % 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 (0.26), residues: 1002 helix: 1.65 (0.25), residues: 410 sheet: 0.50 (0.34), residues: 216 loop : 0.03 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS R 264 PHE 0.015 0.001 PHE N 68 TYR 0.016 0.001 TYR R 187 ARG 0.006 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 165 time to evaluate : 0.991 Fit side-chains REVERT: B 59 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.6257 (t80) REVERT: B 175 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7202 (mt0) REVERT: B 212 ASP cc_start: 0.7435 (t0) cc_final: 0.7022 (t0) REVERT: B 217 MET cc_start: 0.6567 (ttt) cc_final: 0.6144 (ptm) REVERT: B 234 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: B 262 MET cc_start: 0.8408 (tpp) cc_final: 0.7977 (tpp) REVERT: B 303 ASP cc_start: 0.7544 (m-30) cc_final: 0.7257 (m-30) REVERT: B 325 MET cc_start: 0.7897 (mmt) cc_final: 0.7453 (mmt) REVERT: N 46 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7011 (mm-30) REVERT: R 93 VAL cc_start: 0.4254 (OUTLIER) cc_final: 0.3749 (t) REVERT: R 220 ARG cc_start: 0.6222 (mmt90) cc_final: 0.5680 (mmm-85) REVERT: R 314 LYS cc_start: 0.7176 (pttp) cc_final: 0.6499 (ptmt) outliers start: 38 outliers final: 27 residues processed: 187 average time/residue: 0.2442 time to fit residues: 59.9626 Evaluate side-chains 186 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 0.0970 chunk 18 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 0.0870 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 267 GLN B 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8239 Z= 0.164 Angle : 0.484 6.143 11149 Z= 0.267 Chirality : 0.041 0.131 1274 Planarity : 0.004 0.068 1415 Dihedral : 4.194 49.538 1118 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.41 % Allowed : 15.93 % Favored : 79.66 % 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: 1.16 (0.27), residues: 1002 helix: 1.69 (0.26), residues: 409 sheet: 0.48 (0.34), residues: 215 loop : 0.03 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS R 264 PHE 0.013 0.001 PHE N 68 TYR 0.019 0.001 TYR N 117 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 161 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 263 THR cc_start: 0.5495 (OUTLIER) cc_final: 0.5082 (t) REVERT: A 264 ASN cc_start: 0.7050 (t0) cc_final: 0.6663 (t0) REVERT: A 333 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7893 (mtm-85) REVERT: B 9 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7874 (tp-100) REVERT: B 19 ARG cc_start: 0.6893 (mmt-90) cc_final: 0.6636 (mmt-90) REVERT: B 59 TYR cc_start: 0.6840 (OUTLIER) cc_final: 0.6426 (t80) REVERT: B 212 ASP cc_start: 0.7471 (t0) cc_final: 0.7035 (t0) REVERT: B 217 MET cc_start: 0.6496 (ttt) cc_final: 0.6212 (ptm) REVERT: B 234 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8242 (m-80) REVERT: B 303 ASP cc_start: 0.7589 (m-30) cc_final: 0.7292 (m-30) REVERT: B 325 MET cc_start: 0.7893 (mmt) cc_final: 0.7428 (mmt) REVERT: G 41 CYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7007 (p) REVERT: R 93 VAL cc_start: 0.4084 (OUTLIER) cc_final: 0.3577 (t) REVERT: R 220 ARG cc_start: 0.6233 (mmt90) cc_final: 0.5680 (mmm-85) REVERT: R 241 MET cc_start: 0.5344 (ttm) cc_final: 0.4672 (ppp) outliers start: 39 outliers final: 30 residues processed: 183 average time/residue: 0.2404 time to fit residues: 57.1309 Evaluate side-chains 191 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 267 GLN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8239 Z= 0.155 Angle : 0.480 6.979 11149 Z= 0.261 Chirality : 0.040 0.131 1274 Planarity : 0.004 0.049 1415 Dihedral : 4.153 49.046 1118 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.86 % Allowed : 15.71 % Favored : 79.44 % 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: 1.12 (0.27), residues: 1002 helix: 1.69 (0.26), residues: 410 sheet: 0.28 (0.34), residues: 220 loop : 0.09 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS R 264 PHE 0.012 0.001 PHE B 199 TYR 0.016 0.001 TYR R 187 ARG 0.005 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 162 time to evaluate : 0.931 Fit side-chains REVERT: A 263 THR cc_start: 0.5581 (OUTLIER) cc_final: 0.5156 (t) REVERT: A 356 ARG cc_start: 0.6332 (OUTLIER) cc_final: 0.5992 (mtt90) REVERT: B 9 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7838 (tp-100) REVERT: B 19 ARG cc_start: 0.7021 (mmt-90) cc_final: 0.6762 (mmt-90) REVERT: B 43 ILE cc_start: 0.9079 (mm) cc_final: 0.8853 (mm) REVERT: B 59 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.6371 (t80) REVERT: B 212 ASP cc_start: 0.7142 (t0) cc_final: 0.6818 (t0) REVERT: B 234 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: B 303 ASP cc_start: 0.7503 (m-30) cc_final: 0.7203 (m-30) REVERT: B 325 MET cc_start: 0.7866 (mmt) cc_final: 0.7408 (mmt) REVERT: G 21 MET cc_start: 0.8187 (mmm) cc_final: 0.7928 (mmm) REVERT: G 22 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.6087 (mp0) REVERT: G 41 CYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7017 (p) REVERT: N 98 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7149 (ttp80) REVERT: R 93 VAL cc_start: 0.4030 (OUTLIER) cc_final: 0.3499 (t) REVERT: R 220 ARG cc_start: 0.6081 (mmt90) cc_final: 0.5582 (ttm-80) REVERT: R 241 MET cc_start: 0.5333 (ttm) cc_final: 0.4562 (ppp) REVERT: R 314 LYS cc_start: 0.7005 (pttp) cc_final: 0.6330 (ptmt) outliers start: 43 outliers final: 31 residues processed: 188 average time/residue: 0.2482 time to fit residues: 60.3005 Evaluate side-chains 201 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 65 optimal weight: 0.0070 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 overall best weight: 1.0804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8239 Z= 0.175 Angle : 0.503 6.200 11149 Z= 0.272 Chirality : 0.041 0.132 1274 Planarity : 0.004 0.045 1415 Dihedral : 4.207 49.266 1118 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.08 % Allowed : 15.82 % Favored : 79.10 % 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 (0.27), residues: 1002 helix: 1.79 (0.26), residues: 403 sheet: 0.31 (0.35), residues: 213 loop : -0.05 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS R 264 PHE 0.013 0.001 PHE B 199 TYR 0.015 0.001 TYR R 187 ARG 0.009 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 158 time to evaluate : 0.992 Fit side-chains REVERT: A 263 THR cc_start: 0.5895 (OUTLIER) cc_final: 0.5521 (t) REVERT: A 333 ARG cc_start: 0.8081 (mtm-85) cc_final: 0.7825 (mtm-85) REVERT: A 356 ARG cc_start: 0.6361 (OUTLIER) cc_final: 0.6023 (mtt90) REVERT: B 9 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7865 (tp-100) REVERT: B 43 ILE cc_start: 0.9059 (mm) cc_final: 0.8735 (mm) REVERT: B 59 TYR cc_start: 0.6820 (OUTLIER) cc_final: 0.6454 (t80) REVERT: B 98 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8238 (t) REVERT: B 212 ASP cc_start: 0.7271 (t0) cc_final: 0.6937 (t0) REVERT: B 234 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: B 303 ASP cc_start: 0.7478 (m-30) cc_final: 0.7177 (m-30) REVERT: B 325 MET cc_start: 0.7865 (mmt) cc_final: 0.7402 (mmt) REVERT: G 21 MET cc_start: 0.8214 (mmm) cc_final: 0.8012 (mmm) REVERT: G 22 GLU cc_start: 0.6336 (mp0) cc_final: 0.6023 (mp0) REVERT: N 98 ARG cc_start: 0.7479 (ttp80) cc_final: 0.7041 (ttp80) REVERT: R 93 VAL cc_start: 0.4078 (OUTLIER) cc_final: 0.3556 (t) REVERT: R 150 THR cc_start: 0.8013 (p) cc_final: 0.7575 (m) REVERT: R 220 ARG cc_start: 0.6170 (mmt90) cc_final: 0.5723 (ttm-80) REVERT: R 288 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7334 (mp) REVERT: R 314 LYS cc_start: 0.7011 (pttp) cc_final: 0.6376 (ptmt) outliers start: 45 outliers final: 33 residues processed: 185 average time/residue: 0.2392 time to fit residues: 57.2634 Evaluate side-chains 197 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 157 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 307 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 53 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 239 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8239 Z= 0.247 Angle : 0.551 6.233 11149 Z= 0.300 Chirality : 0.042 0.133 1274 Planarity : 0.004 0.051 1415 Dihedral : 4.495 50.822 1118 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.54 % Allowed : 16.27 % Favored : 78.19 % 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: 0.89 (0.26), residues: 1002 helix: 1.65 (0.26), residues: 402 sheet: 0.11 (0.34), residues: 218 loop : -0.15 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.002 PHE B 199 TYR 0.016 0.002 TYR B 264 ARG 0.009 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 162 time to evaluate : 0.962 Fit side-chains REVERT: A 263 THR cc_start: 0.6083 (OUTLIER) cc_final: 0.5843 (t) REVERT: A 264 ASN cc_start: 0.7194 (t0) cc_final: 0.6693 (t0) REVERT: A 339 TYR cc_start: 0.7682 (m-80) cc_final: 0.7361 (m-80) REVERT: A 356 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.5957 (mtt90) REVERT: B 9 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7863 (tp-100) REVERT: B 43 ILE cc_start: 0.8985 (mm) cc_final: 0.8672 (mm) REVERT: B 59 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.6588 (t80) REVERT: B 98 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8238 (t) REVERT: B 212 ASP cc_start: 0.7374 (t0) cc_final: 0.7030 (t0) REVERT: B 228 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: B 234 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: B 303 ASP cc_start: 0.7485 (m-30) cc_final: 0.7185 (m-30) REVERT: B 325 MET cc_start: 0.7943 (mmt) cc_final: 0.7433 (mmt) REVERT: G 22 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: N 98 ARG cc_start: 0.7494 (ttp80) cc_final: 0.7276 (ttp80) REVERT: R 93 VAL cc_start: 0.4433 (OUTLIER) cc_final: 0.3933 (t) REVERT: R 220 ARG cc_start: 0.6315 (mmt90) cc_final: 0.5905 (ttm-80) REVERT: R 288 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7378 (mp) REVERT: R 314 LYS cc_start: 0.7077 (pttp) cc_final: 0.6451 (ptmt) outliers start: 49 outliers final: 37 residues processed: 191 average time/residue: 0.2379 time to fit residues: 58.9353 Evaluate side-chains 204 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 158 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 307 GLN Chi-restraints excluded: chain R residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 8.9990 chunk 65 optimal weight: 0.4980 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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: 0.6763 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8239 Z= 0.273 Angle : 0.573 9.798 11149 Z= 0.309 Chirality : 0.043 0.133 1274 Planarity : 0.005 0.048 1415 Dihedral : 4.646 52.698 1118 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.31 % Allowed : 16.72 % Favored : 77.97 % 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 (0.26), residues: 1002 helix: 1.57 (0.26), residues: 402 sheet: -0.06 (0.34), residues: 216 loop : -0.24 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.002 PHE B 199 TYR 0.017 0.002 TYR B 264 ARG 0.009 0.001 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 0.936 Fit side-chains REVERT: A 264 ASN cc_start: 0.7259 (t0) cc_final: 0.6994 (t0) REVERT: A 347 ARG cc_start: 0.6348 (ptp90) cc_final: 0.6137 (mtp-110) REVERT: A 356 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.5975 (mtt90) REVERT: B 9 GLN cc_start: 0.8113 (tp-100) cc_final: 0.7846 (tp-100) REVERT: B 43 ILE cc_start: 0.8899 (mm) cc_final: 0.8599 (mm) REVERT: B 98 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8278 (t) REVERT: B 212 ASP cc_start: 0.7346 (t0) cc_final: 0.7043 (t0) REVERT: B 228 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7938 (m-30) REVERT: B 234 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: B 303 ASP cc_start: 0.7499 (m-30) cc_final: 0.7195 (m-30) REVERT: B 325 MET cc_start: 0.7936 (mmt) cc_final: 0.7432 (mmt) REVERT: G 22 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: G 41 CYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7135 (p) REVERT: R 93 VAL cc_start: 0.4441 (OUTLIER) cc_final: 0.3942 (t) REVERT: R 150 THR cc_start: 0.8237 (p) cc_final: 0.7722 (m) REVERT: R 220 ARG cc_start: 0.6329 (mmt90) cc_final: 0.5926 (ttm-80) REVERT: R 288 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7444 (mp) REVERT: R 314 LYS cc_start: 0.7121 (pttp) cc_final: 0.6536 (ptmt) outliers start: 47 outliers final: 37 residues processed: 190 average time/residue: 0.2416 time to fit residues: 59.7061 Evaluate side-chains 200 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 155 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 264 HIS Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 307 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 0.0770 chunk 80 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.0170 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 239 ASN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.182320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.136075 restraints weight = 8952.419| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.03 r_work: 0.3751 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8239 Z= 0.144 Angle : 0.500 9.451 11149 Z= 0.268 Chirality : 0.040 0.133 1274 Planarity : 0.004 0.059 1415 Dihedral : 4.323 52.010 1118 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.29 % Allowed : 17.40 % Favored : 78.31 % 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: 1.13 (0.27), residues: 1002 helix: 1.98 (0.26), residues: 399 sheet: 0.09 (0.35), residues: 207 loop : -0.08 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS R 264 PHE 0.012 0.001 PHE B 235 TYR 0.016 0.001 TYR N 117 ARG 0.009 0.001 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2243.33 seconds wall clock time: 41 minutes 18.67 seconds (2478.67 seconds total)