Starting phenix.real_space_refine on Fri Jan 19 09:31:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/01_2024/7tj9_25920_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/01_2024/7tj9_25920.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/01_2024/7tj9_25920_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/01_2024/7tj9_25920_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/01_2024/7tj9_25920_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/01_2024/7tj9_25920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/01_2024/7tj9_25920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/01_2024/7tj9_25920_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj9_25920/01_2024/7tj9_25920_updated.pdb" } resolution = 2.9 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= 0.036 sd= 0.047 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 P 4 5.49 5 S 92 5.16 5 C 7379 2.51 5 N 1642 2.21 5 O 1858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 982": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10975 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 9054 Classifications: {'peptide': 1111} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 1072} Chain breaks: 3 Chain: "B" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1322 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 515 Unusual residues: {'CLR': 2, 'NAG': 1, 'PEV': 3, 'PLM': 8, 'POV': 3, 'Q7G': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.64, per 1000 atoms: 0.61 Number of scatterers: 10975 At special positions: 0 Unit cell: (126.963, 114.15, 114.15, 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) S 92 16.00 P 4 15.00 O 1858 8.00 N 1642 7.00 C 7379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 267 " - pdb=" SG CYS A 307 " distance=2.05 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 664 " distance=2.03 Simple disulfide: pdb=" SG CYS A 696 " - pdb=" SG CYS A 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A1087 " - pdb=" SG CYS A1107 " distance=2.03 Simple disulfide: pdb=" SG CYS A1451 " - pdb=" SG CYS A1466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 48 " distance=2.03 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 120 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A2412 " - " ASN A1103 " " NAG B 301 " - " ASN B 121 " " NAG B 302 " - " ASN B 95 " " NAG B 303 " - " ASN B 113 " " NAG B 304 " - " ASN B 109 " " NAG C 1 " - " ASN A 309 " Time building additional restraints: 5.03 Conformation dependent library (CDL) restraints added in 2.0 seconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 5 sheets defined 62.9% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 144 through 166 Processing helix chain 'A' and resid 179 through 195 removed outlier: 3.506A pdb=" N LEU A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 218 removed outlier: 3.518A pdb=" N THR A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 221 through 259 removed outlier: 3.787A pdb=" N ILE A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 355 through 365 Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.988A pdb=" N ILE A 372 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 403 Processing helix chain 'A' and resid 508 through 524 Processing helix chain 'A' and resid 532 through 558 removed outlier: 3.749A pdb=" N LEU A 537 " --> pdb=" O THR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 removed outlier: 3.706A pdb=" N PHE A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 584 Processing helix chain 'A' and resid 596 through 609 removed outlier: 4.282A pdb=" N MET A 600 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR A 609 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 655 removed outlier: 4.732A pdb=" N VAL A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ALA A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASN A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 691 through 699 removed outlier: 3.597A pdb=" N ASP A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 732 Proline residue: A 707 - end of helix Processing helix chain 'A' and resid 922 through 932 Processing helix chain 'A' and resid 934 through 953 removed outlier: 3.906A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 952 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A 953 " --> pdb=" O GLY A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 990 removed outlier: 3.646A pdb=" N ILE A 966 " --> pdb=" O LYS A 962 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 996 Processing helix chain 'A' and resid 999 through 1018 removed outlier: 3.920A pdb=" N LYS A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1040 removed outlier: 3.602A pdb=" N SER A1028 " --> pdb=" O PRO A1025 " (cutoff:3.500A) Proline residue: A1034 - end of helix removed outlier: 3.628A pdb=" N GLN A1040 " --> pdb=" O VAL A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1055 Processing helix chain 'A' and resid 1059 through 1080 Processing helix chain 'A' and resid 1104 through 1108 Processing helix chain 'A' and resid 1128 through 1139 Processing helix chain 'A' and resid 1144 through 1153 Processing helix chain 'A' and resid 1167 through 1179 removed outlier: 3.748A pdb=" N ILE A1174 " --> pdb=" O CYS A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1203 Processing helix chain 'A' and resid 1212 through 1226 removed outlier: 4.313A pdb=" N LYS A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A1217 " --> pdb=" O LYS A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1249 removed outlier: 3.588A pdb=" N THR A1249 " --> pdb=" O PHE A1245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1245 through 1249' Processing helix chain 'A' and resid 1251 through 1270 removed outlier: 3.530A pdb=" N MET A1268 " --> pdb=" O GLN A1264 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET A1269 " --> pdb=" O ALA A1265 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE A1270 " --> pdb=" O ILE A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1304 removed outlier: 3.524A pdb=" N ILE A1281 " --> pdb=" O LEU A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1334 Proline residue: A1332 - end of helix Processing helix chain 'A' and resid 1344 through 1357 removed outlier: 3.574A pdb=" N SER A1351 " --> pdb=" O LEU A1347 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG A1352 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE A1353 " --> pdb=" O LEU A1349 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A1354 " --> pdb=" O LEU A1350 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N HIS A1355 " --> pdb=" O SER A1351 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N MET A1356 " --> pdb=" O ARG A1352 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU A1357 " --> pdb=" O ILE A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1402 Proline residue: A1372 - end of helix Proline residue: A1378 - end of helix Processing helix chain 'A' and resid 1420 through 1431 Processing helix chain 'A' and resid 1436 through 1446 removed outlier: 4.015A pdb=" N ASN A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N SER A1446 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1502 Processing helix chain 'B' and resid 153 through 185 Processing sheet with id= A, first strand: chain 'A' and resid 265 through 269 Processing sheet with id= B, first strand: chain 'A' and resid 1086 through 1088 Processing sheet with id= C, first strand: chain 'B' and resid 34 through 36 removed outlier: 6.666A pdb=" N ARG B 144 " --> pdb=" O ALA B 35 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 41 through 43 Processing sheet with id= E, first strand: chain 'B' and resid 134 through 143 removed outlier: 3.592A pdb=" N VAL B 122 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR B 75 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR B 64 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU B 73 " --> pdb=" O TYR B 64 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1659 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: 3.36 Time building geometry restraints manager: 5.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3070 1.34 - 1.46: 2878 1.46 - 1.59: 4970 1.59 - 1.71: 177 1.71 - 1.84: 157 Bond restraints: 11252 Sorted by residual: bond pdb=" C29 POV A2403 " pdb="C210 POV A2403 " ideal model delta sigma weight residual 1.333 1.638 -0.305 2.00e-02 2.50e+03 2.33e+02 bond pdb=" C13 Q7G A2418 " pdb=" C14 Q7G A2418 " ideal model delta sigma weight residual 1.599 1.318 0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C07 Q7G A2418 " pdb=" C15 Q7G A2418 " ideal model delta sigma weight residual 1.779 1.515 0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" O14 POV A2408 " pdb=" P POV A2408 " ideal model delta sigma weight residual 1.496 1.748 -0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C73 Q7G A2418 " pdb=" O72 Q7G A2418 " ideal model delta sigma weight residual 1.338 1.577 -0.239 2.00e-02 2.50e+03 1.42e+02 ... (remaining 11247 not shown) Histogram of bond angle deviations from ideal: 90.40 - 99.16: 5 99.16 - 107.92: 450 107.92 - 116.68: 7278 116.68 - 125.43: 7257 125.43 - 134.19: 185 Bond angle restraints: 15175 Sorted by residual: angle pdb=" C74 Q7G A2418 " pdb=" C73 Q7G A2418 " pdb=" C76 Q7G A2418 " ideal model delta sigma weight residual 109.92 131.39 -21.47 3.00e+00 1.11e-01 5.12e+01 angle pdb=" C51 Q7G A2418 " pdb=" C61 Q7G A2418 " pdb=" O61 Q7G A2418 " ideal model delta sigma weight residual 109.51 130.90 -21.39 3.00e+00 1.11e-01 5.08e+01 angle pdb=" C74 Q7G A2418 " pdb=" C73 Q7G A2418 " pdb=" O80 Q7G A2418 " ideal model delta sigma weight residual 109.75 90.40 19.35 3.00e+00 1.11e-01 4.16e+01 angle pdb=" O3P PEV A2411 " pdb=" P PEV A2411 " pdb=" O4P PEV A2411 " ideal model delta sigma weight residual 93.57 110.99 -17.42 3.00e+00 1.11e-01 3.37e+01 angle pdb=" O3P PEV A2401 " pdb=" P PEV A2401 " pdb=" O4P PEV A2401 " ideal model delta sigma weight residual 93.57 110.49 -16.92 3.00e+00 1.11e-01 3.18e+01 ... (remaining 15170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.44: 6515 29.44 - 58.87: 292 58.87 - 88.31: 37 88.31 - 117.74: 27 117.74 - 147.18: 5 Dihedral angle restraints: 6876 sinusoidal: 3148 harmonic: 3728 Sorted by residual: dihedral pdb=" CB CYS A 267 " pdb=" SG CYS A 267 " pdb=" SG CYS A 307 " pdb=" CB CYS A 307 " ideal model delta sinusoidal sigma weight residual -86.00 -155.57 69.57 1 1.00e+01 1.00e-02 6.25e+01 dihedral pdb=" CA HIS A 560 " pdb=" C HIS A 560 " pdb=" N PRO A 561 " pdb=" CA PRO A 561 " ideal model delta harmonic sigma weight residual 180.00 -151.62 -28.38 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" C4B Q7G A2418 " pdb=" C5B Q7G A2418 " pdb=" C6B Q7G A2418 " pdb=" O6B Q7G A2418 " ideal model delta sinusoidal sigma weight residual 143.94 -68.88 -147.18 1 3.00e+01 1.11e-03 1.96e+01 ... (remaining 6873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 1712 0.180 - 0.360: 10 0.360 - 0.540: 3 0.540 - 0.720: 1 0.720 - 0.900: 1 Chirality restraints: 1727 Sorted by residual: chirality pdb=" C1 NAG B 301 " pdb=" ND2 ASN B 121 " pdb=" C2 NAG B 301 " pdb=" O5 NAG B 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" C02 Q7G A2418 " pdb=" C03 Q7G A2418 " pdb=" C06 Q7G A2418 " pdb=" C10 Q7G A2418 " both_signs ideal model delta sigma weight residual False 2.14 2.84 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C2 POV A2402 " pdb=" C1 POV A2402 " pdb=" C3 POV A2402 " pdb=" O21 POV A2402 " both_signs ideal model delta sigma weight residual False 2.43 2.92 -0.49 2.00e-01 2.50e+01 5.99e+00 ... (remaining 1724 not shown) Planarity restraints: 1797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " -0.331 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG B 303 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " -0.140 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " 0.511 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 301 " 0.289 2.00e-02 2.50e+03 2.42e-01 7.32e+02 pdb=" C7 NAG B 301 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG B 301 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG B 301 " -0.412 2.00e-02 2.50e+03 pdb=" O7 NAG B 301 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2412 " 0.239 2.00e-02 2.50e+03 2.00e-01 5.00e+02 pdb=" C7 NAG A2412 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG A2412 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG A2412 " -0.336 2.00e-02 2.50e+03 pdb=" O7 NAG A2412 " -0.006 2.00e-02 2.50e+03 ... (remaining 1794 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 433 2.71 - 3.26: 11177 3.26 - 3.81: 17225 3.81 - 4.35: 21641 4.35 - 4.90: 36754 Nonbonded interactions: 87230 Sorted by model distance: nonbonded pdb=" O THR A 207 " pdb=" OG1 THR A 210 " model vdw 2.167 2.440 nonbonded pdb=" OD1 ASN A 149 " pdb=" OH TYR A 196 " model vdw 2.210 2.440 nonbonded pdb=" O ALA A 642 " pdb=" OG SER A 677 " model vdw 2.238 2.440 nonbonded pdb=" O THR B 111 " pdb=" OD1 ASP B 114 " model vdw 2.253 3.040 nonbonded pdb=" O PHE A1072 " pdb=" OH TYR A1172 " model vdw 2.297 2.440 ... (remaining 87225 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.220 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.750 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.017 0.305 11252 Z= 1.121 Angle : 1.022 21.472 15175 Z= 0.443 Chirality : 0.056 0.900 1727 Planarity : 0.013 0.287 1791 Dihedral : 18.478 147.177 4445 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.09 % Allowed : 0.78 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.24), residues: 1263 helix: 1.16 (0.18), residues: 770 sheet: -1.47 (0.61), residues: 74 loop : -1.64 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A1144 HIS 0.005 0.001 HIS B 131 PHE 0.031 0.002 PHE A1031 TYR 0.021 0.002 TYR A 354 ARG 0.004 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.8162 (tp30) cc_final: 0.7845 (tp30) REVERT: B 37 GLN cc_start: 0.8270 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 97 SER cc_start: 0.9245 (m) cc_final: 0.9030 (m) outliers start: 1 outliers final: 1 residues processed: 265 average time/residue: 0.9138 time to fit residues: 267.1396 Evaluate side-chains 213 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 ASN A 676 HIS ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 ASN A1287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11252 Z= 0.232 Angle : 0.628 13.756 15175 Z= 0.305 Chirality : 0.043 0.275 1727 Planarity : 0.005 0.083 1791 Dihedral : 16.674 177.936 2005 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.99 % Allowed : 12.14 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.93 (0.24), residues: 1263 helix: 1.69 (0.18), residues: 764 sheet: -0.87 (0.61), residues: 76 loop : -1.10 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1144 HIS 0.004 0.001 HIS B 131 PHE 0.020 0.001 PHE A 578 TYR 0.011 0.001 TYR A 354 ARG 0.002 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 230 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.8685 (ttt) cc_final: 0.8383 (ttt) REVERT: A 400 GLU cc_start: 0.8133 (tp30) cc_final: 0.7846 (tp30) REVERT: A 596 ARG cc_start: 0.7635 (tmt170) cc_final: 0.7393 (tmt170) REVERT: A 974 ILE cc_start: 0.8492 (mm) cc_final: 0.8226 (mt) REVERT: A 1078 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.6995 (m-30) REVERT: A 1279 MET cc_start: 0.8150 (tpp) cc_final: 0.7924 (mtp) REVERT: A 1490 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8427 (mtp) REVERT: B 28 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: B 37 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7824 (tm-30) REVERT: B 83 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6509 (pp20) REVERT: B 97 SER cc_start: 0.9249 (m) cc_final: 0.8984 (m) outliers start: 46 outliers final: 21 residues processed: 247 average time/residue: 0.9395 time to fit residues: 257.6876 Evaluate side-chains 239 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 214 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1288 SER Chi-restraints excluded: chain A residue 1470 SER Chi-restraints excluded: chain A residue 1490 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.0670 chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11252 Z= 0.364 Angle : 0.676 11.747 15175 Z= 0.327 Chirality : 0.044 0.243 1727 Planarity : 0.005 0.073 1791 Dihedral : 15.215 139.620 2003 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.29 % Allowed : 14.48 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.99 (0.24), residues: 1263 helix: 1.65 (0.18), residues: 759 sheet: -0.24 (0.66), residues: 64 loop : -0.95 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1144 HIS 0.005 0.001 HIS B 131 PHE 0.017 0.002 PHE A 268 TYR 0.016 0.002 TYR A1168 ARG 0.003 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 223 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.8144 (tp30) cc_final: 0.7842 (tp30) REVERT: A 596 ARG cc_start: 0.7757 (tmt170) cc_final: 0.7424 (tmt170) REVERT: A 625 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8353 (p) REVERT: A 974 ILE cc_start: 0.8443 (mm) cc_final: 0.8196 (mt) REVERT: A 1078 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7184 (m-30) REVERT: A 1086 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7553 (pt0) REVERT: B 28 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: B 32 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: B 37 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7841 (tt0) REVERT: B 83 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6481 (pp20) REVERT: B 97 SER cc_start: 0.9231 (m) cc_final: 0.9009 (m) outliers start: 61 outliers final: 34 residues processed: 245 average time/residue: 0.9076 time to fit residues: 246.9975 Evaluate side-chains 256 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1199 HIS Chi-restraints excluded: chain A residue 1207 ASN Chi-restraints excluded: chain A residue 1221 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1288 SER Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1470 SER Chi-restraints excluded: chain A residue 1490 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN A 998 ASN ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11252 Z= 0.303 Angle : 0.616 10.890 15175 Z= 0.302 Chirality : 0.042 0.221 1727 Planarity : 0.004 0.065 1791 Dihedral : 14.255 125.597 2003 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.46 % Allowed : 15.78 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1263 helix: 1.71 (0.18), residues: 766 sheet: -0.60 (0.61), residues: 76 loop : -0.86 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1144 HIS 0.004 0.001 HIS B 131 PHE 0.015 0.002 PHE A1245 TYR 0.013 0.001 TYR A1168 ARG 0.002 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 226 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.6773 (OUTLIER) cc_final: 0.6418 (t0) REVERT: A 400 GLU cc_start: 0.8130 (tp30) cc_final: 0.7846 (tp30) REVERT: A 578 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6510 (t80) REVERT: A 596 ARG cc_start: 0.7727 (tmt170) cc_final: 0.7387 (tmt170) REVERT: A 974 ILE cc_start: 0.8492 (mm) cc_final: 0.8210 (mt) REVERT: A 1031 PHE cc_start: 0.8440 (m-10) cc_final: 0.8157 (m-10) REVERT: A 1086 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: A 1490 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8249 (ttp) REVERT: B 32 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: B 37 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7782 (tt0) REVERT: B 44 ARG cc_start: 0.8380 (ttm170) cc_final: 0.7573 (ttm-80) REVERT: B 83 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6489 (pp20) REVERT: B 97 SER cc_start: 0.9222 (m) cc_final: 0.9003 (m) outliers start: 63 outliers final: 34 residues processed: 255 average time/residue: 0.9034 time to fit residues: 255.1667 Evaluate side-chains 258 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 218 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1199 HIS Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1490 MET Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 145 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 998 ASN ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11252 Z= 0.222 Angle : 0.568 10.241 15175 Z= 0.278 Chirality : 0.041 0.271 1727 Planarity : 0.004 0.058 1791 Dihedral : 13.583 120.251 2003 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.64 % Allowed : 16.05 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.30 (0.24), residues: 1263 helix: 1.89 (0.18), residues: 769 sheet: -0.53 (0.60), residues: 76 loop : -0.80 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1118 HIS 0.003 0.001 HIS B 131 PHE 0.013 0.001 PHE A 201 TYR 0.010 0.001 TYR A1168 ARG 0.002 0.000 ARG A1463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 227 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7063 (t80) REVERT: A 183 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8546 (tp) REVERT: A 400 GLU cc_start: 0.8109 (tp30) cc_final: 0.7823 (tp30) REVERT: A 596 ARG cc_start: 0.7622 (tmt170) cc_final: 0.7350 (tmt170) REVERT: A 974 ILE cc_start: 0.8552 (mm) cc_final: 0.8276 (mt) REVERT: A 1031 PHE cc_start: 0.8469 (m-10) cc_final: 0.8153 (m-10) REVERT: A 1078 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7014 (m-30) REVERT: A 1086 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7532 (pt0) REVERT: A 1490 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8213 (ttp) REVERT: B 32 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: B 37 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7693 (tt0) REVERT: B 83 GLU cc_start: 0.7102 (pp20) cc_final: 0.6282 (pp20) outliers start: 65 outliers final: 34 residues processed: 262 average time/residue: 0.9101 time to fit residues: 263.9966 Evaluate side-chains 260 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 220 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 958 MET Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1086 GLU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1207 ASN Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1288 SER Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1490 MET Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 998 ASN ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11252 Z= 0.178 Angle : 0.541 9.913 15175 Z= 0.265 Chirality : 0.040 0.214 1727 Planarity : 0.004 0.052 1791 Dihedral : 13.143 115.354 2003 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.60 % Allowed : 17.35 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.49 (0.24), residues: 1263 helix: 2.08 (0.18), residues: 766 sheet: -0.33 (0.62), residues: 72 loop : -0.81 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1118 HIS 0.002 0.001 HIS B 131 PHE 0.013 0.001 PHE A 201 TYR 0.009 0.001 TYR A1475 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 232 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7504 (t80) REVERT: A 183 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8493 (tp) REVERT: A 400 GLU cc_start: 0.8120 (tp30) cc_final: 0.7875 (tp30) REVERT: A 596 ARG cc_start: 0.7518 (tmt170) cc_final: 0.7258 (tmt170) REVERT: A 974 ILE cc_start: 0.8533 (mm) cc_final: 0.8265 (mt) REVERT: A 1031 PHE cc_start: 0.8418 (m-10) cc_final: 0.8185 (m-10) REVERT: A 1036 ARG cc_start: 0.8457 (tpt90) cc_final: 0.8188 (tpt-90) REVERT: A 1078 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6988 (m-30) REVERT: A 1086 GLU cc_start: 0.7882 (pt0) cc_final: 0.7516 (pt0) REVERT: A 1365 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.8005 (p) REVERT: A 1490 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8166 (ttp) REVERT: B 32 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: B 37 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7627 (tt0) REVERT: B 83 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6285 (pp20) outliers start: 53 outliers final: 31 residues processed: 261 average time/residue: 0.9383 time to fit residues: 271.3291 Evaluate side-chains 266 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 228 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1199 HIS Chi-restraints excluded: chain A residue 1207 ASN Chi-restraints excluded: chain A residue 1221 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1243 PHE Chi-restraints excluded: chain A residue 1288 SER Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1490 MET Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 145 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 922 ASN A 998 ASN A1275 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11252 Z= 0.201 Angle : 0.550 9.741 15175 Z= 0.269 Chirality : 0.040 0.223 1727 Planarity : 0.004 0.049 1791 Dihedral : 12.987 113.977 2003 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.25 % Allowed : 19.69 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.49 (0.24), residues: 1263 helix: 2.06 (0.18), residues: 768 sheet: -0.23 (0.62), residues: 72 loop : -0.81 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 935 HIS 0.002 0.001 HIS B 131 PHE 0.013 0.001 PHE A1245 TYR 0.008 0.001 TYR A1475 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 227 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7532 (t80) REVERT: A 400 GLU cc_start: 0.8120 (tp30) cc_final: 0.7886 (tp30) REVERT: A 578 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6523 (t80) REVERT: A 596 ARG cc_start: 0.7521 (tmt170) cc_final: 0.7249 (tmt170) REVERT: A 974 ILE cc_start: 0.8544 (mm) cc_final: 0.8279 (mt) REVERT: A 1031 PHE cc_start: 0.8429 (m-10) cc_final: 0.8227 (m-10) REVERT: A 1036 ARG cc_start: 0.8493 (tpt90) cc_final: 0.8003 (tpt-90) REVERT: A 1078 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.7016 (m-30) REVERT: A 1086 GLU cc_start: 0.7887 (pt0) cc_final: 0.7514 (pt0) REVERT: A 1371 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8406 (mt) REVERT: A 1490 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8184 (ttp) REVERT: B 32 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: B 37 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7641 (tt0) REVERT: B 83 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6270 (pp20) outliers start: 49 outliers final: 33 residues processed: 256 average time/residue: 0.9079 time to fit residues: 257.4809 Evaluate side-chains 260 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 220 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1199 HIS Chi-restraints excluded: chain A residue 1207 ASN Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1288 SER Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1490 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.0770 chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 998 ASN A1162 HIS ** A1166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11252 Z= 0.146 Angle : 0.517 9.556 15175 Z= 0.253 Chirality : 0.039 0.194 1727 Planarity : 0.004 0.046 1791 Dihedral : 12.640 109.084 2003 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.56 % Allowed : 20.56 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.75 (0.24), residues: 1263 helix: 2.27 (0.18), residues: 765 sheet: 0.14 (0.63), residues: 70 loop : -0.76 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 935 HIS 0.002 0.001 HIS A1367 PHE 0.015 0.001 PHE A 201 TYR 0.010 0.001 TYR A1475 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 235 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.6964 (t80) REVERT: A 400 GLU cc_start: 0.8071 (tp30) cc_final: 0.7798 (tp30) REVERT: A 578 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6501 (t80) REVERT: A 596 ARG cc_start: 0.7479 (tmt170) cc_final: 0.7259 (tmt170) REVERT: A 624 TRP cc_start: 0.7746 (OUTLIER) cc_final: 0.7299 (t60) REVERT: A 955 ASP cc_start: 0.8331 (p0) cc_final: 0.8020 (p0) REVERT: A 974 ILE cc_start: 0.8513 (mm) cc_final: 0.8249 (OUTLIER) REVERT: A 1036 ARG cc_start: 0.8489 (tpt90) cc_final: 0.8110 (mmm160) REVERT: A 1086 GLU cc_start: 0.7717 (pt0) cc_final: 0.7383 (pt0) REVERT: B 37 GLN cc_start: 0.7800 (tm-30) cc_final: 0.7557 (tt0) REVERT: B 83 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6256 (pp20) outliers start: 41 outliers final: 26 residues processed: 256 average time/residue: 0.8107 time to fit residues: 229.2932 Evaluate side-chains 258 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 624 TRP Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1207 ASN Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1288 SER Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.2404 > 50: distance: 5 - 28: 17.479 distance: 13 - 36: 7.968 distance: 18 - 44: 17.752 distance: 21 - 28: 20.803 distance: 28 - 29: 19.564 distance: 29 - 30: 3.154 distance: 29 - 32: 6.273 distance: 30 - 31: 6.799 distance: 30 - 36: 12.954 distance: 32 - 33: 11.807 distance: 32 - 34: 14.301 distance: 33 - 35: 31.412 distance: 36 - 37: 7.812 distance: 37 - 38: 8.368 distance: 37 - 40: 10.803 distance: 38 - 39: 7.269 distance: 38 - 44: 9.006 distance: 40 - 41: 23.352 distance: 40 - 42: 14.906 distance: 41 - 43: 3.477 distance: 44 - 45: 9.620 distance: 45 - 46: 6.293 distance: 45 - 48: 14.044 distance: 46 - 47: 18.000 distance: 46 - 49: 9.726 distance: 49 - 50: 20.216 distance: 50 - 51: 5.802 distance: 50 - 53: 26.105 distance: 51 - 52: 23.557 distance: 51 - 57: 34.601 distance: 53 - 54: 6.700 distance: 54 - 55: 15.250 distance: 55 - 56: 21.722 distance: 57 - 58: 13.453 distance: 58 - 59: 19.873 distance: 58 - 61: 7.514 distance: 59 - 60: 30.949 distance: 59 - 67: 11.980 distance: 61 - 62: 12.675 distance: 62 - 63: 9.347 distance: 62 - 64: 33.273 distance: 63 - 65: 34.647 distance: 64 - 66: 27.676 distance: 65 - 66: 22.928 distance: 67 - 68: 10.688 distance: 68 - 69: 13.633 distance: 68 - 71: 14.201 distance: 69 - 70: 27.570 distance: 69 - 74: 12.623 distance: 71 - 72: 25.776 distance: 72 - 73: 30.737 distance: 74 - 75: 15.794 distance: 75 - 76: 4.433 distance: 75 - 78: 12.384 distance: 76 - 77: 17.816 distance: 76 - 86: 8.550 distance: 77 - 113: 12.797 distance: 78 - 79: 9.828 distance: 79 - 80: 13.879 distance: 79 - 81: 9.288 distance: 80 - 82: 5.353 distance: 81 - 83: 4.888 distance: 82 - 84: 3.522 distance: 83 - 84: 4.465 distance: 84 - 85: 6.536 distance: 86 - 87: 12.216 distance: 87 - 88: 15.276 distance: 88 - 89: 14.921 distance: 88 - 90: 27.035 distance: 90 - 91: 40.511 distance: 91 - 92: 27.960 distance: 91 - 94: 39.076 distance: 92 - 93: 36.890 distance: 92 - 102: 26.534 distance: 94 - 95: 23.356 distance: 95 - 96: 11.615 distance: 95 - 97: 5.249 distance: 96 - 98: 5.693 distance: 97 - 99: 11.683 distance: 98 - 100: 10.771 distance: 99 - 100: 9.402 distance: 100 - 101: 15.459 distance: 102 - 103: 6.698 distance: 103 - 104: 30.417 distance: 103 - 106: 39.236 distance: 104 - 105: 9.051 distance: 104 - 113: 30.749 distance: 106 - 107: 27.515 distance: 107 - 108: 22.600 distance: 107 - 109: 11.208 distance: 108 - 110: 28.973 distance: 109 - 111: 12.131 distance: 110 - 112: 5.826 distance: 111 - 112: 7.259