Starting phenix.real_space_refine on Fri Mar 15 10:36:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi3_33850/03_2024/7yi3_33850.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi3_33850/03_2024/7yi3_33850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi3_33850/03_2024/7yi3_33850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi3_33850/03_2024/7yi3_33850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi3_33850/03_2024/7yi3_33850.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi3_33850/03_2024/7yi3_33850.pdb" } resolution = 3.3 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= 0.002 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 Zn 5 6.06 5 S 66 5.16 5 C 7300 2.51 5 N 1919 2.21 5 O 2135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 805": "OE1" <-> "OE2" Residue "A GLU 1027": "OE1" <-> "OE2" Residue "A PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11425 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4258 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 7, 'TRANS': 498} Chain breaks: 5 Chain: "B" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2923 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "C" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1473 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 174} Chain: "D" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2588 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 298} Chain breaks: 5 Chain: "E" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 178 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10169 SG CYS D 417 69.984 60.745 32.968 1.00 40.15 S ATOM 10196 SG CYS D 420 71.715 57.465 33.828 1.00 55.87 S ATOM 10452 SG CYS D 451 71.468 60.228 36.443 1.00 62.19 S ATOM 9108 SG CYS D 263 35.162 94.931 38.011 1.00 93.60 S ATOM 9125 SG CYS D 266 38.264 92.690 37.687 1.00 76.39 S ATOM 9278 SG CYS D 286 38.493 95.811 39.869 1.00 74.17 S ATOM 9413 SG CYS D 303 27.320 102.172 35.913 1.00108.66 S ATOM 9436 SG CYS D 306 23.561 104.664 35.015 1.00110.05 S ATOM 10357 SG CYS D 440 64.800 70.261 28.800 1.00 45.36 S ATOM 10383 SG CYS D 443 67.690 69.873 26.226 1.00 52.08 S ATOM 10572 SG CYS D 466 68.566 70.907 29.657 1.00 62.77 S Time building chain proxies: 6.55, per 1000 atoms: 0.57 Number of scatterers: 11425 At special positions: 0 Unit cell: (120.157, 139.643, 107.168, 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) Zn 5 29.99 S 66 16.00 O 2135 8.00 N 1919 7.00 C 7300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.58 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" ND1 HIS D 448 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 420 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 417 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 451 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" ND1 HIS D 283 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 286 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 263 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 303 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 306 " pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" NE2 HIS D 469 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 466 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 443 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 440 " Number of angles added : 9 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 7 sheets defined 54.5% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 678 through 694 removed outlier: 3.724A pdb=" N GLU A 684 " --> pdb=" O HIS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.506A pdb=" N LEU A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 722 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 771 through 777 Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.866A pdb=" N ALA A 789 " --> pdb=" O HIS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 838 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 891 through 922 removed outlier: 4.094A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 removed outlier: 3.884A pdb=" N LEU A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 removed outlier: 4.142A pdb=" N THR A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 943 Processing helix chain 'A' and resid 944 through 961 Processing helix chain 'A' and resid 983 through 999 Processing helix chain 'A' and resid 1003 through 1023 Processing helix chain 'A' and resid 1141 through 1164 removed outlier: 4.157A pdb=" N MET A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1174 Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 4.162A pdb=" N MET A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1220 through 1233 Processing helix chain 'A' and resid 1236 through 1240 removed outlier: 3.682A pdb=" N LEU A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 Processing helix chain 'A' and resid 1259 through 1276 Processing helix chain 'A' and resid 1280 through 1294 removed outlier: 4.373A pdb=" N ILE A1284 " --> pdb=" O ALA A1280 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.794A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 54 removed outlier: 3.858A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 115 through 137 Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.594A pdb=" N ARG B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 287 through 300 removed outlier: 4.592A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.520A pdb=" N TYR B 346 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'C' and resid 225 through 241 Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.936A pdb=" N GLN C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 297 removed outlier: 3.798A pdb=" N LEU C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 279 " --> pdb=" O GLN C 275 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.607A pdb=" N ASP C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.501A pdb=" N SER C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 369 removed outlier: 3.522A pdb=" N GLN C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.599A pdb=" N MET C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 182 through 187 removed outlier: 4.419A pdb=" N GLY D 186 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 331 removed outlier: 3.758A pdb=" N LYS D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN D 331 " --> pdb=" O ILE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 removed outlier: 4.374A pdb=" N ASP D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 Processing helix chain 'D' and resid 430 through 434 Processing helix chain 'D' and resid 544 through 562 removed outlier: 3.668A pdb=" N LYS D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR D 549 " --> pdb=" O ASN D 545 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE D 552 " --> pdb=" O LYS D 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 563 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 removed outlier: 3.566A pdb=" N VAL A 783 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.866A pdb=" N VAL B 21 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N TYR B 64 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR B 23 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA B 142 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA5, first strand: chain 'D' and resid 364 through 366 Processing sheet with id=AA6, first strand: chain 'D' and resid 473 through 476 Processing sheet with id=AA7, first strand: chain 'D' and resid 505 through 506 removed outlier: 3.778A pdb=" N TYR D 506 " --> pdb=" O ILE D 539 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3658 1.34 - 1.46: 2696 1.46 - 1.58: 5218 1.58 - 1.70: 0 1.70 - 1.81: 100 Bond restraints: 11672 Sorted by residual: bond pdb=" CG PRO A 786 " pdb=" CD PRO A 786 " ideal model delta sigma weight residual 1.503 1.380 0.123 3.40e-02 8.65e+02 1.31e+01 bond pdb=" CA GLU D 104 " pdb=" C GLU D 104 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.41e-02 5.03e+03 1.17e+00 bond pdb=" CG PRO D 119 " pdb=" CD PRO D 119 " ideal model delta sigma weight residual 1.503 1.538 -0.035 3.40e-02 8.65e+02 1.05e+00 bond pdb=" CG1 ILE A1018 " pdb=" CD1 ILE A1018 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.75e-01 bond pdb=" C ARG A 907 " pdb=" O ARG A 907 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.49e-01 ... (remaining 11667 not shown) Histogram of bond angle deviations from ideal: 92.52 - 100.82: 18 100.82 - 109.13: 649 109.13 - 117.43: 7649 117.43 - 125.74: 7251 125.74 - 134.05: 163 Bond angle restraints: 15730 Sorted by residual: angle pdb=" N PRO A 786 " pdb=" CD PRO A 786 " pdb=" CG PRO A 786 " ideal model delta sigma weight residual 103.20 92.52 10.68 1.50e+00 4.44e-01 5.07e+01 angle pdb=" CA PRO A 786 " pdb=" N PRO A 786 " pdb=" CD PRO A 786 " ideal model delta sigma weight residual 112.00 103.45 8.55 1.40e+00 5.10e-01 3.73e+01 angle pdb=" CA PRO A 786 " pdb=" CB PRO A 786 " pdb=" CG PRO A 786 " ideal model delta sigma weight residual 104.50 96.77 7.73 1.90e+00 2.77e-01 1.65e+01 angle pdb=" CB PRO A 786 " pdb=" CG PRO A 786 " pdb=" CD PRO A 786 " ideal model delta sigma weight residual 106.10 95.14 10.96 3.20e+00 9.77e-02 1.17e+01 angle pdb=" C VAL B 106 " pdb=" CA VAL B 106 " pdb=" CB VAL B 106 " ideal model delta sigma weight residual 111.29 116.84 -5.55 1.64e+00 3.72e-01 1.15e+01 ... (remaining 15725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 6009 17.16 - 34.31: 779 34.31 - 51.47: 190 51.47 - 68.63: 36 68.63 - 85.78: 14 Dihedral angle restraints: 7028 sinusoidal: 2926 harmonic: 4102 Sorted by residual: dihedral pdb=" CA TYR B 347 " pdb=" C TYR B 347 " pdb=" N GLY B 348 " pdb=" CA GLY B 348 " ideal model delta harmonic sigma weight residual 180.00 157.43 22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE C 335 " pdb=" C ILE C 335 " pdb=" N SER C 336 " pdb=" CA SER C 336 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LYS B 153 " pdb=" C LYS B 153 " pdb=" N LYS B 154 " pdb=" CA LYS B 154 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 7025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1127 0.035 - 0.069: 417 0.069 - 0.104: 108 0.104 - 0.139: 35 0.139 - 0.173: 1 Chirality restraints: 1688 Sorted by residual: chirality pdb=" CB ILE D 312 " pdb=" CA ILE D 312 " pdb=" CG1 ILE D 312 " pdb=" CG2 ILE D 312 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CG LEU A 689 " pdb=" CB LEU A 689 " pdb=" CD1 LEU A 689 " pdb=" CD2 LEU A 689 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CB VAL B 106 " pdb=" CA VAL B 106 " pdb=" CG1 VAL B 106 " pdb=" CG2 VAL B 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1685 not shown) Planarity restraints: 2005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 118 " 0.079 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO D 119 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 785 " -0.073 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A 786 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 786 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 786 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR D 439 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C THR D 439 " -0.038 2.00e-02 2.50e+03 pdb=" O THR D 439 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS D 440 " 0.013 2.00e-02 2.50e+03 ... (remaining 2002 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 99 2.59 - 3.17: 9437 3.17 - 3.75: 17650 3.75 - 4.32: 24863 4.32 - 4.90: 40761 Nonbonded interactions: 92810 Sorted by model distance: nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.014 2.230 nonbonded pdb=" OG SER C 313 " pdb=" O LYS C 318 " model vdw 2.090 2.440 nonbonded pdb=" OG SER B 123 " pdb=" OD2 ASP B 165 " model vdw 2.106 2.440 nonbonded pdb=" OD2 ASP B 244 " pdb=" OG SER B 287 " model vdw 2.167 2.440 nonbonded pdb=" O ILE C 342 " pdb=" OG1 THR C 345 " model vdw 2.184 2.440 ... (remaining 92805 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.070 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 35.270 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.003 0.123 11672 Z= 0.165 Angle : 0.523 10.958 15730 Z= 0.286 Chirality : 0.040 0.173 1688 Planarity : 0.005 0.120 2005 Dihedral : 16.299 85.785 4376 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.16 % Allowed : 21.13 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.30 (0.23), residues: 1362 helix: 0.85 (0.20), residues: 712 sheet: -0.58 (0.60), residues: 85 loop : -1.50 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 261 HIS 0.003 0.001 HIS A1252 PHE 0.018 0.001 PHE A1305 TYR 0.015 0.001 TYR B 347 ARG 0.003 0.000 ARG D 369 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 1164 MET cc_start: 0.8311 (ptt) cc_final: 0.8083 (ptt) REVERT: D 548 LYS cc_start: 0.7389 (mtmt) cc_final: 0.6844 (mtmt) outliers start: 2 outliers final: 0 residues processed: 111 average time/residue: 0.2658 time to fit residues: 41.9442 Evaluate side-chains 105 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 124 optimal weight: 0.0980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.0487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11672 Z= 0.151 Angle : 0.475 5.316 15730 Z= 0.255 Chirality : 0.039 0.144 1688 Planarity : 0.004 0.079 2005 Dihedral : 4.406 22.953 1511 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.59 % Allowed : 19.32 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.06 (0.23), residues: 1362 helix: 1.16 (0.19), residues: 707 sheet: -0.32 (0.62), residues: 84 loop : -1.35 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1223 HIS 0.004 0.001 HIS B 49 PHE 0.010 0.001 PHE B 113 TYR 0.015 0.001 TYR B 347 ARG 0.003 0.000 ARG D 369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 1.415 Fit side-chains REVERT: A 818 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: A 1197 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6419 (p0) REVERT: A 1288 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.6039 (mm) REVERT: B 72 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: D 310 ILE cc_start: 0.5985 (OUTLIER) cc_final: 0.5488 (mm) REVERT: D 312 ILE cc_start: 0.5851 (OUTLIER) cc_final: 0.5505 (mt) outliers start: 33 outliers final: 13 residues processed: 142 average time/residue: 0.2495 time to fit residues: 51.3802 Evaluate side-chains 120 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11672 Z= 0.164 Angle : 0.474 5.351 15730 Z= 0.255 Chirality : 0.039 0.147 1688 Planarity : 0.004 0.063 2005 Dihedral : 4.385 22.492 1511 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.06 % Allowed : 21.05 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.14 (0.23), residues: 1362 helix: 1.24 (0.19), residues: 706 sheet: -0.24 (0.62), residues: 85 loop : -1.34 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1223 HIS 0.004 0.001 HIS B 49 PHE 0.011 0.001 PHE D 308 TYR 0.016 0.001 TYR B 347 ARG 0.006 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 106 time to evaluate : 1.323 Fit side-chains REVERT: A 1288 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5949 (mm) REVERT: B 72 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.7017 (tt0) REVERT: D 312 ILE cc_start: 0.5924 (OUTLIER) cc_final: 0.5547 (mt) REVERT: D 552 PHE cc_start: 0.7270 (m-10) cc_final: 0.6888 (m-10) outliers start: 39 outliers final: 25 residues processed: 142 average time/residue: 0.2042 time to fit residues: 44.3811 Evaluate side-chains 127 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 516 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11672 Z= 0.154 Angle : 0.468 5.333 15730 Z= 0.251 Chirality : 0.039 0.152 1688 Planarity : 0.004 0.061 2005 Dihedral : 4.340 22.836 1511 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.99 % Allowed : 22.15 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.23 (0.23), residues: 1362 helix: 1.30 (0.19), residues: 709 sheet: -0.18 (0.62), residues: 85 loop : -1.29 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 261 HIS 0.003 0.001 HIS B 49 PHE 0.010 0.001 PHE B 113 TYR 0.015 0.001 TYR B 347 ARG 0.006 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 107 time to evaluate : 1.408 Fit side-chains REVERT: A 818 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: A 1197 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6445 (p0) REVERT: A 1288 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5988 (mm) REVERT: B 72 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7025 (tt0) REVERT: D 312 ILE cc_start: 0.5904 (OUTLIER) cc_final: 0.5514 (mt) REVERT: D 552 PHE cc_start: 0.7283 (m-10) cc_final: 0.6886 (m-10) outliers start: 38 outliers final: 25 residues processed: 142 average time/residue: 0.2170 time to fit residues: 46.9119 Evaluate side-chains 132 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN C 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11672 Z= 0.298 Angle : 0.571 6.972 15730 Z= 0.305 Chirality : 0.043 0.158 1688 Planarity : 0.005 0.070 2005 Dihedral : 4.829 24.501 1511 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.30 % Allowed : 22.94 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.14 (0.23), residues: 1362 helix: 1.00 (0.19), residues: 709 sheet: -0.45 (0.57), residues: 96 loop : -1.47 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 447 HIS 0.004 0.001 HIS A1252 PHE 0.017 0.002 PHE D 308 TYR 0.022 0.002 TYR B 347 ARG 0.005 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 102 time to evaluate : 1.364 Fit side-chains REVERT: A 1197 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6578 (p0) REVERT: A 1288 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5930 (mm) REVERT: B 238 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8066 (mt) REVERT: D 312 ILE cc_start: 0.5946 (OUTLIER) cc_final: 0.5610 (mt) REVERT: D 552 PHE cc_start: 0.7243 (m-10) cc_final: 0.6928 (m-10) outliers start: 42 outliers final: 28 residues processed: 140 average time/residue: 0.2210 time to fit residues: 47.1403 Evaluate side-chains 129 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 110 optimal weight: 0.0270 chunk 61 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11672 Z= 0.151 Angle : 0.479 6.144 15730 Z= 0.257 Chirality : 0.040 0.178 1688 Planarity : 0.004 0.063 2005 Dihedral : 4.490 23.610 1511 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.38 % Allowed : 23.02 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.12 (0.23), residues: 1362 helix: 1.19 (0.19), residues: 715 sheet: -0.31 (0.57), residues: 95 loop : -1.33 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 261 HIS 0.003 0.001 HIS B 49 PHE 0.011 0.001 PHE B 113 TYR 0.014 0.001 TYR B 347 ARG 0.005 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 109 time to evaluate : 1.407 Fit side-chains REVERT: A 719 TRP cc_start: 0.6441 (t60) cc_final: 0.6133 (t60) REVERT: A 818 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: A 1197 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6502 (p0) REVERT: B 238 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8019 (mt) REVERT: D 312 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5512 (mt) REVERT: D 552 PHE cc_start: 0.7199 (m-10) cc_final: 0.6892 (m-10) outliers start: 43 outliers final: 31 residues processed: 147 average time/residue: 0.2140 time to fit residues: 47.1965 Evaluate side-chains 135 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 0.0050 chunk 14 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11672 Z= 0.148 Angle : 0.475 5.507 15730 Z= 0.255 Chirality : 0.040 0.168 1688 Planarity : 0.004 0.072 2005 Dihedral : 4.371 22.643 1511 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.38 % Allowed : 22.94 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.25 (0.23), residues: 1362 helix: 1.31 (0.19), residues: 709 sheet: -0.23 (0.57), residues: 95 loop : -1.28 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 261 HIS 0.003 0.001 HIS A1252 PHE 0.010 0.001 PHE B 113 TYR 0.015 0.001 TYR B 347 ARG 0.004 0.000 ARG D 369 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 103 time to evaluate : 1.362 Fit side-chains REVERT: A 719 TRP cc_start: 0.6554 (t60) cc_final: 0.6250 (t60) REVERT: A 818 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8008 (m-30) REVERT: A 1197 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.6515 (p0) REVERT: A 1288 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5950 (mm) REVERT: D 312 ILE cc_start: 0.6027 (OUTLIER) cc_final: 0.5589 (mt) REVERT: D 552 PHE cc_start: 0.7195 (m-10) cc_final: 0.6882 (m-10) outliers start: 43 outliers final: 32 residues processed: 141 average time/residue: 0.2111 time to fit residues: 45.3514 Evaluate side-chains 135 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 99 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11672 Z= 0.254 Angle : 0.539 6.714 15730 Z= 0.288 Chirality : 0.042 0.171 1688 Planarity : 0.005 0.079 2005 Dihedral : 4.673 23.821 1511 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.38 % Allowed : 23.41 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.04 (0.23), residues: 1362 helix: 1.14 (0.19), residues: 709 sheet: -0.30 (0.57), residues: 95 loop : -1.37 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1223 HIS 0.004 0.001 HIS A1252 PHE 0.013 0.002 PHE D 308 TYR 0.021 0.002 TYR B 347 ARG 0.004 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 99 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 719 TRP cc_start: 0.6585 (t60) cc_final: 0.6230 (t60) REVERT: A 1197 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6538 (p0) REVERT: B 238 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8024 (mt) REVERT: D 312 ILE cc_start: 0.5902 (OUTLIER) cc_final: 0.5549 (mt) REVERT: D 552 PHE cc_start: 0.7201 (m-10) cc_final: 0.6920 (m-10) outliers start: 43 outliers final: 33 residues processed: 138 average time/residue: 0.1952 time to fit residues: 41.3959 Evaluate side-chains 133 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 97 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1227 SER Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.4980 chunk 123 optimal weight: 0.4980 chunk 126 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 111 optimal weight: 0.0970 chunk 116 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11672 Z= 0.141 Angle : 0.470 5.719 15730 Z= 0.253 Chirality : 0.040 0.145 1688 Planarity : 0.004 0.072 2005 Dihedral : 4.367 23.005 1511 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.75 % Allowed : 23.96 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1362 helix: 1.32 (0.19), residues: 710 sheet: -0.18 (0.57), residues: 95 loop : -1.28 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 261 HIS 0.003 0.001 HIS B 49 PHE 0.010 0.001 PHE A 708 TYR 0.012 0.001 TYR B 347 ARG 0.004 0.000 ARG A1273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: A 1197 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6480 (p0) REVERT: D 312 ILE cc_start: 0.5999 (OUTLIER) cc_final: 0.5557 (mt) REVERT: D 552 PHE cc_start: 0.7164 (m-10) cc_final: 0.6822 (m-10) outliers start: 35 outliers final: 30 residues processed: 130 average time/residue: 0.2143 time to fit residues: 42.3178 Evaluate side-chains 131 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 0.0970 chunk 66 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11672 Z= 0.145 Angle : 0.470 5.532 15730 Z= 0.252 Chirality : 0.040 0.148 1688 Planarity : 0.004 0.078 2005 Dihedral : 4.300 22.374 1511 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.75 % Allowed : 24.19 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.34 (0.23), residues: 1362 helix: 1.39 (0.19), residues: 708 sheet: -0.13 (0.57), residues: 95 loop : -1.24 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 719 HIS 0.003 0.001 HIS A1252 PHE 0.010 0.001 PHE A1021 TYR 0.014 0.001 TYR B 347 ARG 0.004 0.000 ARG A1273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 106 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: A 719 TRP cc_start: 0.6750 (t60) cc_final: 0.6279 (t60) REVERT: A 1197 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6488 (p0) REVERT: B 305 MET cc_start: 0.7441 (ttt) cc_final: 0.7153 (mtp) REVERT: D 312 ILE cc_start: 0.5976 (OUTLIER) cc_final: 0.5538 (mt) REVERT: D 552 PHE cc_start: 0.7113 (m-10) cc_final: 0.6782 (m-10) outliers start: 35 outliers final: 31 residues processed: 137 average time/residue: 0.2069 time to fit residues: 42.3943 Evaluate side-chains 135 residues out of total 1273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 102 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1197 ASP Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.130294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.107370 restraints weight = 19174.196| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.95 r_work: 0.3349 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11672 Z= 0.177 Angle : 0.492 5.841 15730 Z= 0.263 Chirality : 0.040 0.180 1688 Planarity : 0.004 0.080 2005 Dihedral : 4.398 22.783 1511 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.91 % Allowed : 24.19 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.27 (0.23), residues: 1362 helix: 1.32 (0.19), residues: 711 sheet: -0.21 (0.57), residues: 95 loop : -1.27 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 719 HIS 0.003 0.001 HIS A1252 PHE 0.012 0.001 PHE A1021 TYR 0.017 0.001 TYR B 347 ARG 0.004 0.000 ARG A1273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.30 seconds wall clock time: 45 minutes 2.55 seconds (2702.55 seconds total)