Starting phenix.real_space_refine on Tue Feb 13 23:50:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f54_31457/02_2024/7f54_31457_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f54_31457/02_2024/7f54_31457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f54_31457/02_2024/7f54_31457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f54_31457/02_2024/7f54_31457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f54_31457/02_2024/7f54_31457_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f54_31457/02_2024/7f54_31457_updated.pdb" } resolution = 3.0 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= 0.007 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 5155 2.51 5 N 1403 2.21 5 O 1513 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 PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 308": "OE1" <-> "OE2" Residue "R GLU 315": "OE1" <-> "OE2" 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: 8134 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: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 114 Classifications: {'peptide': 13} Modifications used: {'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 5.09, per 1000 atoms: 0.63 Number of scatterers: 8134 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 1513 8.00 N 1403 7.00 C 5155 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=2.03 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: 5.10 Conformation dependent library (CDL) restraints added in 1.7 seconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN L 7 " Number of C-beta restraints generated: 1948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 11 sheets defined 39.2% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 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: 3.548A 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: 3.787A 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 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: 4.303A 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: 7.038A 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: 4.384A 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) 405 hydrogen bonds defined for protein. 1026 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: 2.22 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2628 1.34 - 1.46: 1919 1.46 - 1.58: 3651 1.58 - 1.71: 0 1.71 - 1.83: 87 Bond restraints: 8285 Sorted by residual: bond pdb=" C PHE A 273 " pdb=" O PHE A 273 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.17e-02 7.31e+03 3.12e+00 bond pdb=" C ARG R 147 " pdb=" O ARG R 147 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.17e-02 7.31e+03 3.10e+00 bond pdb=" C ALA R 144 " pdb=" O ALA R 144 " ideal model delta sigma weight residual 1.237 1.217 0.019 1.17e-02 7.31e+03 2.70e+00 bond pdb=" C LYS A 34 " pdb=" O LYS A 34 " ideal model delta sigma weight residual 1.237 1.218 0.018 1.17e-02 7.31e+03 2.44e+00 bond pdb=" C ALA R 70 " pdb=" N LYS R 71 " ideal model delta sigma weight residual 1.331 1.353 -0.023 1.48e-02 4.57e+03 2.36e+00 ... (remaining 8280 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.74: 207 106.74 - 113.56: 4560 113.56 - 120.37: 3241 120.37 - 127.19: 3127 127.19 - 134.01: 78 Bond angle restraints: 11213 Sorted by residual: angle pdb=" N LYS B 78 " pdb=" CA LYS B 78 " pdb=" C LYS B 78 " ideal model delta sigma weight residual 108.69 117.01 -8.32 1.77e+00 3.19e-01 2.21e+01 angle pdb=" N LEU R 286 " pdb=" CA LEU R 286 " pdb=" C LEU R 286 " ideal model delta sigma weight residual 113.41 107.78 5.63 1.22e+00 6.72e-01 2.13e+01 angle pdb=" C ILE R 143 " pdb=" CA ILE R 143 " pdb=" CB ILE R 143 " ideal model delta sigma weight residual 111.97 106.80 5.17 1.28e+00 6.10e-01 1.63e+01 angle pdb=" N CYS N 96 " pdb=" CA CYS N 96 " pdb=" C CYS N 96 " ideal model delta sigma weight residual 109.76 103.42 6.34 1.64e+00 3.72e-01 1.49e+01 angle pdb=" N LYS R 71 " pdb=" CA LYS R 71 " pdb=" C LYS R 71 " ideal model delta sigma weight residual 113.16 117.67 -4.51 1.24e+00 6.50e-01 1.33e+01 ... (remaining 11208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4656 17.58 - 35.16: 226 35.16 - 52.74: 49 52.74 - 70.32: 19 70.32 - 87.91: 5 Dihedral angle restraints: 4955 sinusoidal: 1948 harmonic: 3007 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 4952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 967 0.055 - 0.111: 257 0.111 - 0.166: 46 0.166 - 0.222: 8 0.222 - 0.277: 2 Chirality restraints: 1280 Sorted by residual: chirality pdb=" CA TYR R 157 " pdb=" N TYR R 157 " pdb=" C TYR R 157 " pdb=" CB TYR R 157 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA HIS R 158 " pdb=" N HIS R 158 " pdb=" C HIS R 158 " pdb=" CB HIS R 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 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 2.31 0.20 2.00e-01 2.50e+01 9.64e-01 ... (remaining 1277 not shown) Planarity restraints: 1424 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 1421 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 687 2.74 - 3.28: 8141 3.28 - 3.82: 13176 3.82 - 4.36: 16605 4.36 - 4.90: 28429 Nonbonded interactions: 67038 Sorted by model distance: nonbonded pdb=" O ASP B 163 " pdb=" OD1 ASP B 163 " model vdw 2.194 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.216 2.440 nonbonded pdb=" OG SER R 58 " pdb=" OG SER R 94 " model vdw 2.244 2.440 nonbonded pdb=" OG SER R 116 " pdb=" N PHE R 117 " model vdw 2.259 2.520 nonbonded pdb=" OD2 ASP R 122 " pdb=" CG NLE L 4 " model vdw 2.302 3.440 ... (remaining 67033 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.980 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 28.570 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8285 Z= 0.290 Angle : 0.892 9.374 11213 Z= 0.554 Chirality : 0.053 0.277 1280 Planarity : 0.006 0.041 1424 Dihedral : 11.931 87.906 2995 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.89 % Favored : 97.91 % Rotamer: Outliers : 0.22 % Allowed : 3.37 % Favored : 96.40 % 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 (0.26), residues: 1006 helix: 0.98 (0.24), residues: 413 sheet: 0.79 (0.35), residues: 223 loop : 0.75 (0.33), residues: 370 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 0.003 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) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 237 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7460 (tt0) cc_final: 0.7157 (tp-100) REVERT: A 293 LYS cc_start: 0.8370 (mttt) cc_final: 0.7755 (tmtt) REVERT: B 20 ASP cc_start: 0.6349 (m-30) cc_final: 0.5819 (p0) REVERT: B 265 SER cc_start: 0.7898 (p) cc_final: 0.7538 (m) REVERT: R 145 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7668 (t) REVERT: R 204 MET cc_start: 0.6074 (mtt) cc_final: 0.5602 (mmt) outliers start: 2 outliers final: 1 residues processed: 239 average time/residue: 0.9895 time to fit residues: 252.8143 Evaluate side-chains 151 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 0.0470 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 176 GLN B 259 GLN G 24 ASN R 72 ASN R 264 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8285 Z= 0.205 Angle : 0.587 7.205 11213 Z= 0.322 Chirality : 0.043 0.148 1280 Planarity : 0.005 0.035 1424 Dihedral : 4.292 15.935 1126 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.26 % Allowed : 14.61 % Favored : 82.13 % 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: 1.67 (0.26), residues: 1006 helix: 1.73 (0.25), residues: 405 sheet: 1.10 (0.33), residues: 212 loop : 0.61 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.009 0.001 HIS R 264 PHE 0.017 0.002 PHE N 68 TYR 0.014 0.001 TYR R 80 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7457 (tt) REVERT: A 293 LYS cc_start: 0.8528 (mttt) cc_final: 0.7795 (tmtt) REVERT: A 346 LEU cc_start: 0.7574 (mt) cc_final: 0.7321 (mt) REVERT: B 20 ASP cc_start: 0.6657 (m-30) cc_final: 0.6143 (p0) REVERT: B 186 ASP cc_start: 0.5665 (OUTLIER) cc_final: 0.5432 (m-30) REVERT: N 77 ASN cc_start: 0.7818 (m-40) cc_final: 0.7596 (t0) outliers start: 29 outliers final: 9 residues processed: 177 average time/residue: 0.9398 time to fit residues: 179.0716 Evaluate side-chains 135 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain R residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 0.0040 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 0.0060 chunk 89 optimal weight: 0.8980 overall best weight: 0.9410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS G 24 ASN R 264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8285 Z= 0.173 Angle : 0.537 7.568 11213 Z= 0.288 Chirality : 0.042 0.145 1280 Planarity : 0.004 0.036 1424 Dihedral : 4.125 15.203 1123 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.71 % Allowed : 16.74 % Favored : 79.55 % 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: 1.62 (0.26), residues: 1006 helix: 1.79 (0.25), residues: 405 sheet: 1.09 (0.33), residues: 211 loop : 0.43 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.010 0.001 HIS R 264 PHE 0.027 0.002 PHE B 241 TYR 0.013 0.001 TYR B 85 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.7384 (pp30) cc_final: 0.6706 (pp30) REVERT: A 293 LYS cc_start: 0.8523 (mttt) cc_final: 0.7739 (tmtt) REVERT: A 339 TYR cc_start: 0.7810 (m-80) cc_final: 0.7587 (m-80) REVERT: A 342 ARG cc_start: 0.6839 (ttp-170) cc_final: 0.6209 (ttm-80) REVERT: A 346 LEU cc_start: 0.7646 (mt) cc_final: 0.7407 (mt) REVERT: B 20 ASP cc_start: 0.6521 (m-30) cc_final: 0.6181 (p0) REVERT: B 298 ASP cc_start: 0.6946 (t70) cc_final: 0.6608 (t70) REVERT: G 24 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7205 (p0) outliers start: 33 outliers final: 13 residues processed: 163 average time/residue: 0.8905 time to fit residues: 156.9631 Evaluate side-chains 143 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 10.0000 chunk 47 optimal weight: 0.0010 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 1.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 239 ASN A 387 HIS ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS R 76 HIS R 264 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8285 Z= 0.243 Angle : 0.581 7.666 11213 Z= 0.315 Chirality : 0.044 0.212 1280 Planarity : 0.005 0.037 1424 Dihedral : 4.453 23.705 1123 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.93 % Allowed : 19.10 % Favored : 76.97 % 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: 1.20 (0.26), residues: 1006 helix: 1.52 (0.25), residues: 404 sheet: 0.85 (0.34), residues: 205 loop : 0.12 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.013 0.002 HIS R 264 PHE 0.018 0.002 PHE B 335 TYR 0.015 0.002 TYR N 95 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.8398 (mttt) cc_final: 0.7556 (tmtt) REVERT: A 339 TYR cc_start: 0.7826 (m-80) cc_final: 0.7581 (m-80) REVERT: A 342 ARG cc_start: 0.6851 (ttp-170) cc_final: 0.6189 (ttm-80) REVERT: A 346 LEU cc_start: 0.7661 (mt) cc_final: 0.7352 (mt) REVERT: A 358 TYR cc_start: 0.7603 (m-80) cc_final: 0.7399 (m-10) REVERT: B 226 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6890 (mt-10) REVERT: G 21 MET cc_start: 0.8074 (mpt) cc_final: 0.7872 (mpt) REVERT: R 72 ASN cc_start: 0.7015 (OUTLIER) cc_final: 0.6324 (m-40) REVERT: R 297 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.6899 (tp) outliers start: 35 outliers final: 17 residues processed: 163 average time/residue: 0.9372 time to fit residues: 165.1239 Evaluate side-chains 145 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN G 24 ASN R 264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8285 Z= 0.154 Angle : 0.522 8.153 11213 Z= 0.279 Chirality : 0.041 0.144 1280 Planarity : 0.004 0.035 1424 Dihedral : 4.174 15.487 1123 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.70 % Allowed : 21.01 % Favored : 76.29 % 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: 1.28 (0.26), residues: 1006 helix: 1.61 (0.25), residues: 407 sheet: 0.91 (0.35), residues: 205 loop : 0.13 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.011 0.001 HIS R 264 PHE 0.017 0.001 PHE A 376 TYR 0.012 0.001 TYR N 95 ARG 0.004 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.8369 (mttt) cc_final: 0.7302 (tmtt) REVERT: A 339 TYR cc_start: 0.7756 (m-80) cc_final: 0.7490 (m-80) REVERT: A 342 ARG cc_start: 0.6790 (ttp-170) cc_final: 0.6149 (ttm-80) REVERT: A 346 LEU cc_start: 0.7807 (mt) cc_final: 0.7551 (mt) REVERT: B 226 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6975 (mt-10) REVERT: B 239 ASN cc_start: 0.7103 (m110) cc_final: 0.6398 (t0) REVERT: B 336 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7940 (mt) REVERT: G 21 MET cc_start: 0.8166 (mpt) cc_final: 0.7941 (mpt) REVERT: R 72 ASN cc_start: 0.6959 (OUTLIER) cc_final: 0.6244 (m-40) REVERT: R 273 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6913 (mp10) outliers start: 24 outliers final: 15 residues processed: 153 average time/residue: 0.9845 time to fit residues: 161.7858 Evaluate side-chains 143 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 292 ASN R 264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8285 Z= 0.151 Angle : 0.532 9.468 11213 Z= 0.279 Chirality : 0.041 0.159 1280 Planarity : 0.004 0.034 1424 Dihedral : 4.062 17.101 1123 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.58 % Allowed : 21.91 % Favored : 75.51 % 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: 1.38 (0.26), residues: 1006 helix: 1.71 (0.26), residues: 404 sheet: 0.92 (0.34), residues: 214 loop : 0.18 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.011 0.001 HIS R 264 PHE 0.020 0.001 PHE B 241 TYR 0.014 0.001 TYR B 111 ARG 0.006 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.8373 (mttt) cc_final: 0.7231 (tmtt) REVERT: A 339 TYR cc_start: 0.7760 (m-80) cc_final: 0.7519 (m-80) REVERT: A 342 ARG cc_start: 0.6715 (ttp-170) cc_final: 0.6208 (ttm-80) REVERT: B 226 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6819 (mt-10) REVERT: B 336 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7937 (mt) REVERT: R 72 ASN cc_start: 0.6993 (OUTLIER) cc_final: 0.6324 (m-40) REVERT: R 273 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6823 (mp10) REVERT: R 297 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.6782 (tp) outliers start: 23 outliers final: 10 residues processed: 150 average time/residue: 1.0169 time to fit residues: 163.6507 Evaluate side-chains 140 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.0570 chunk 70 optimal weight: 0.0040 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.4312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 292 ASN B 176 GLN R 97 ASN R 264 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8285 Z= 0.143 Angle : 0.536 9.354 11213 Z= 0.279 Chirality : 0.041 0.168 1280 Planarity : 0.004 0.032 1424 Dihedral : 3.913 15.109 1123 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.15 % Allowed : 22.70 % Favored : 74.16 % 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: 1.47 (0.27), residues: 1006 helix: 1.78 (0.26), residues: 404 sheet: 0.93 (0.35), residues: 215 loop : 0.25 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 339 HIS 0.011 0.001 HIS R 264 PHE 0.017 0.001 PHE B 241 TYR 0.013 0.001 TYR R 268 ARG 0.003 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 293 LYS cc_start: 0.8353 (mttt) cc_final: 0.7258 (tmtt) REVERT: A 339 TYR cc_start: 0.7720 (m-80) cc_final: 0.7483 (m-80) REVERT: A 342 ARG cc_start: 0.6569 (ttp-170) cc_final: 0.6092 (ttm-80) REVERT: B 16 ASN cc_start: 0.7857 (m-40) cc_final: 0.7654 (m-40) REVERT: B 59 TYR cc_start: 0.5963 (OUTLIER) cc_final: 0.5414 (m-80) REVERT: B 226 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6748 (mt-10) REVERT: R 223 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6661 (mp) REVERT: R 273 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6839 (mp10) outliers start: 28 outliers final: 13 residues processed: 151 average time/residue: 0.9549 time to fit residues: 155.2474 Evaluate side-chains 138 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 273 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN R 264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8285 Z= 0.245 Angle : 0.599 8.993 11213 Z= 0.316 Chirality : 0.043 0.160 1280 Planarity : 0.004 0.031 1424 Dihedral : 4.168 16.035 1123 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.26 % Allowed : 23.37 % Favored : 73.37 % 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: 1.28 (0.26), residues: 1006 helix: 1.69 (0.26), residues: 404 sheet: 0.79 (0.35), residues: 206 loop : 0.11 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 339 HIS 0.013 0.001 HIS R 264 PHE 0.030 0.002 PHE A 315 TYR 0.016 0.002 TYR N 95 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.8398 (mttt) cc_final: 0.7182 (tmtt) REVERT: A 342 ARG cc_start: 0.6662 (ttp-170) cc_final: 0.6212 (ttm-80) REVERT: B 59 TYR cc_start: 0.6148 (OUTLIER) cc_final: 0.5617 (m-80) REVERT: B 226 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6910 (mt-10) REVERT: B 251 ARG cc_start: 0.7458 (mtt90) cc_final: 0.7171 (ttm110) REVERT: B 336 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7969 (mt) REVERT: R 204 MET cc_start: 0.5739 (pp-130) cc_final: 0.5286 (mtp) REVERT: R 223 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7081 (mt) REVERT: R 273 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6887 (mp10) REVERT: R 297 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7159 (tp) outliers start: 29 outliers final: 14 residues processed: 145 average time/residue: 0.9771 time to fit residues: 152.3367 Evaluate side-chains 142 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.2980 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 292 ASN R 264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8285 Z= 0.159 Angle : 0.565 10.051 11213 Z= 0.292 Chirality : 0.041 0.167 1280 Planarity : 0.004 0.032 1424 Dihedral : 4.009 14.763 1123 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.58 % Allowed : 24.72 % Favored : 72.70 % 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: 1.42 (0.27), residues: 1006 helix: 1.79 (0.26), residues: 400 sheet: 0.90 (0.35), residues: 205 loop : 0.19 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 339 HIS 0.012 0.001 HIS R 264 PHE 0.027 0.001 PHE A 315 TYR 0.015 0.001 TYR B 111 ARG 0.003 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.8272 (mttt) cc_final: 0.7124 (tmtt) REVERT: A 342 ARG cc_start: 0.6668 (ttp-170) cc_final: 0.6196 (ttm-80) REVERT: B 16 ASN cc_start: 0.8086 (m-40) cc_final: 0.7850 (m-40) REVERT: B 59 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.5607 (m-80) REVERT: B 226 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6782 (mt-10) REVERT: R 183 LEU cc_start: 0.7946 (mm) cc_final: 0.7688 (mp) REVERT: R 223 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.6856 (mt) REVERT: R 273 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6959 (mp10) REVERT: R 297 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7048 (tp) outliers start: 23 outliers final: 12 residues processed: 140 average time/residue: 1.0000 time to fit residues: 150.7063 Evaluate side-chains 135 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 0.0370 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** R 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8285 Z= 0.242 Angle : 0.625 10.601 11213 Z= 0.325 Chirality : 0.043 0.159 1280 Planarity : 0.004 0.031 1424 Dihedral : 4.256 15.978 1123 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.25 % Allowed : 25.62 % Favored : 72.13 % 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: 1.20 (0.27), residues: 1006 helix: 1.49 (0.26), residues: 407 sheet: 0.79 (0.35), residues: 206 loop : 0.19 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 339 HIS 0.014 0.001 HIS R 264 PHE 0.026 0.002 PHE A 315 TYR 0.015 0.002 TYR B 59 ARG 0.003 0.000 ARG A 373 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7177 (tm-30) REVERT: A 342 ARG cc_start: 0.6720 (ttp-170) cc_final: 0.6293 (ttm-80) REVERT: B 59 TYR cc_start: 0.6248 (OUTLIER) cc_final: 0.5728 (m-80) REVERT: B 226 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6924 (mt-10) REVERT: R 183 LEU cc_start: 0.7978 (mm) cc_final: 0.7712 (mp) REVERT: R 223 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7174 (mt) REVERT: R 273 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7061 (mp10) outliers start: 20 outliers final: 12 residues processed: 138 average time/residue: 0.9081 time to fit residues: 135.3813 Evaluate side-chains 132 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 69 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** R 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.185502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.141032 restraints weight = 8826.296| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.70 r_work: 0.3876 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8285 Z= 0.276 Angle : 0.650 10.384 11213 Z= 0.338 Chirality : 0.045 0.187 1280 Planarity : 0.004 0.031 1424 Dihedral : 4.458 15.821 1123 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.91 % Allowed : 26.40 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 1006 helix: 1.46 (0.26), residues: 399 sheet: 0.69 (0.35), residues: 211 loop : 0.10 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 339 HIS 0.014 0.002 HIS R 264 PHE 0.024 0.003 PHE B 241 TYR 0.016 0.002 TYR N 95 ARG 0.003 0.000 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.24 seconds wall clock time: 61 minutes 39.29 seconds (3699.29 seconds total)