Starting phenix.real_space_refine on Fri Jan 19 10:26:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgt_27429/01_2024/8dgt_27429_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgt_27429/01_2024/8dgt_27429.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgt_27429/01_2024/8dgt_27429_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgt_27429/01_2024/8dgt_27429_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgt_27429/01_2024/8dgt_27429_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgt_27429/01_2024/8dgt_27429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgt_27429/01_2024/8dgt_27429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgt_27429/01_2024/8dgt_27429_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgt_27429/01_2024/8dgt_27429_updated.pdb" } resolution = 3.9 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= 0.000 sd= 0.066 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: 9 Type Number sf(0) Gaussians I 1 10.91 5 Zn 2 6.06 5 P 11 5.49 5 Mg 2 5.21 5 S 65 5.16 5 C 6997 2.51 5 N 1910 2.21 5 O 2107 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F ARG 68": "NH1" <-> "NH2" Residue "F GLU 76": "OE1" <-> "OE2" Residue "F GLU 143": "OE1" <-> "OE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 162": "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: 11096 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3455 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2441 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 293} Chain breaks: 1 Chain: "C" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1846 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 5, 'TRANS': 223} Chain: "D" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1833 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 223} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 1398 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1324 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 167, 1324 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1257 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' ZN': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'AGS': 1, 'LCJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 764 SG CYS A 248 44.579 48.524 42.978 1.00 92.22 S ATOM 789 SG CYS A 251 42.579 46.312 43.172 1.00 91.18 S ATOM 971 SG CYS A 272 40.590 49.856 42.034 1.00 91.05 S ATOM 877 SG CYS A 261 53.877 58.376 41.455 1.00 90.50 S ATOM 899 SG CYS A 264 53.885 56.709 44.564 1.00 82.84 S ATOM 1029 SG CYS A 280 54.516 60.397 43.977 1.00 77.32 S Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N MET F 1 " occ=0.76 ... (3 atoms not shown) pdb=" CB MET F 1 " occ=0.76 residue: pdb=" N MET F 67 " occ=0.94 ... (6 atoms not shown) pdb=" CE MET F 67 " occ=0.94 residue: pdb=" N GLN F 70 " occ=0.97 ... (7 atoms not shown) pdb=" NE2 GLN F 70 " occ=0.97 residue: pdb=" N TYR F 71 " occ=0.84 ... (10 atoms not shown) pdb=" OH TYR F 71 " occ=0.84 residue: pdb=" N AGLN F 99 " occ=0.58 ... (16 atoms not shown) pdb=" NE2BGLN F 99 " occ=0.42 residue: pdb=" N GLU F 107 " occ=0.82 ... (7 atoms not shown) pdb=" OE2 GLU F 107 " occ=0.82 residue: pdb=" N GLN F 150 " occ=0.97 ... (7 atoms not shown) pdb=" NE2 GLN F 150 " occ=0.97 Time building chain proxies: 6.55, per 1000 atoms: 0.59 Number of scatterers: 11096 At special positions: 0 Unit cell: (98.88, 94.76, 127.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) I 1 52.95 Zn 2 29.99 S 65 16.00 P 11 15.00 Mg 2 11.99 F 1 9.00 O 2107 8.00 N 1910 7.00 C 6997 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" ND1 HIS A 269 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 272 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 248 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 251 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 280 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 261 " pdb="ZN ZN A 803 " - pdb=" ND1 HIS A 235 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 264 " Number of angles added : 6 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 7 sheets defined 51.4% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 177 through 188 removed outlier: 4.895A pdb=" N LYS A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.711A pdb=" N SER A 273 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 507 removed outlier: 4.012A pdb=" N LYS A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 550 through 570 removed outlier: 3.556A pdb=" N LYS A 570 " --> pdb=" O TYR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 635 through 651 Processing helix chain 'A' and resid 662 through 670 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'B' and resid 44 through 58 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 105 through 119 removed outlier: 3.644A pdb=" N GLN B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N HIS B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 163 through 182 removed outlier: 3.645A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 213 through 221 removed outlier: 4.259A pdb=" N ASN B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 241 through 258 removed outlier: 3.958A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 272 removed outlier: 3.825A pdb=" N GLU B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 268 through 272' Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 332 through 341 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.577A pdb=" N VAL B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 21 through 32 removed outlier: 3.566A pdb=" N THR C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 69 removed outlier: 3.836A pdb=" N ASN C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL C 52 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 101 Processing helix chain 'C' and resid 112 through 130 Processing helix chain 'C' and resid 138 through 159 removed outlier: 3.507A pdb=" N ILE C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 180 Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 212 through 228 Processing helix chain 'D' and resid 3 through 15 Processing helix chain 'D' and resid 19 through 32 removed outlier: 3.543A pdb=" N VAL D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 66 removed outlier: 3.521A pdb=" N LEU D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 removed outlier: 3.511A pdb=" N GLU D 81 " --> pdb=" O GLN D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 112 through 132 removed outlier: 3.540A pdb=" N GLU D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 159 removed outlier: 3.836A pdb=" N ASP D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 180 Processing helix chain 'D' and resid 185 through 201 Processing helix chain 'D' and resid 213 through 229 Processing helix chain 'F' and resid 16 through 25 Processing helix chain 'F' and resid 62 through 74 removed outlier: 4.984A pdb=" N ALA F 66 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 104 removed outlier: 4.669A pdb=" N HIS F 94 " --> pdb=" O PHE F 90 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 Processing helix chain 'F' and resid 152 through 166 Processing sheet with id= A, first strand: chain 'A' and resid 165 through 170 removed outlier: 4.484A pdb=" N VAL A 197 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 237 through 241 Processing sheet with id= C, first strand: chain 'A' and resid 526 through 530 removed outlier: 6.345A pdb=" N LYS A 473 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG A 462 " --> pdb=" O LYS A 473 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 582 through 585 Processing sheet with id= E, first strand: chain 'B' and resid 129 through 135 removed outlier: 6.809A pdb=" N CYS B 142 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA B 132 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER B 140 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR B 134 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER B 86 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS B 70 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 196 through 198 Processing sheet with id= G, first strand: chain 'F' and resid 140 through 143 removed outlier: 3.582A pdb=" N THR F 2 " --> pdb=" O THR F 50 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY F 10 " --> pdb=" O THR F 58 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1547 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 3707 1.37 - 1.55: 7452 1.55 - 1.74: 51 1.74 - 1.92: 102 1.92 - 2.11: 3 Bond restraints: 11315 Sorted by residual: bond pdb=" C GLU A 225 " pdb=" N VAL A 226 " ideal model delta sigma weight residual 1.332 1.475 -0.143 1.36e-02 5.41e+03 1.10e+02 bond pdb=" N3B GNP F 202 " pdb=" PG GNP F 202 " ideal model delta sigma weight residual 1.801 1.711 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" O5' GNP F 202 " pdb=" PA GNP F 202 " ideal model delta sigma weight residual 1.660 1.587 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" O3A GNP F 202 " pdb=" PB GNP F 202 " ideal model delta sigma weight residual 1.687 1.622 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" CA VAL A 157 " pdb=" CB VAL A 157 " ideal model delta sigma weight residual 1.541 1.581 -0.040 1.28e-02 6.10e+03 9.73e+00 ... (remaining 11310 not shown) Histogram of bond angle deviations from ideal: 83.35 - 93.49: 3 93.49 - 103.62: 159 103.62 - 113.75: 6567 113.75 - 123.89: 8308 123.89 - 134.02: 271 Bond angle restraints: 15308 Sorted by residual: angle pdb=" O GLU A 225 " pdb=" C GLU A 225 " pdb=" N VAL A 226 " ideal model delta sigma weight residual 121.70 83.35 38.35 1.84e+00 2.95e-01 4.34e+02 angle pdb=" C MET F 1 " pdb=" N THR F 2 " pdb=" CA THR F 2 " ideal model delta sigma weight residual 122.74 91.23 31.51 1.54e+00 4.22e-01 4.19e+02 angle pdb=" CA MET F 1 " pdb=" C MET F 1 " pdb=" N THR F 2 " ideal model delta sigma weight residual 116.20 89.74 26.46 2.00e+00 2.50e-01 1.75e+02 angle pdb=" CA PRO A 152 " pdb=" N PRO A 152 " pdb=" CD PRO A 152 " ideal model delta sigma weight residual 112.00 98.94 13.06 1.40e+00 5.10e-01 8.70e+01 angle pdb=" CA GLU A 225 " pdb=" C GLU A 225 " pdb=" N VAL A 226 " ideal model delta sigma weight residual 116.18 125.88 -9.70 1.15e+00 7.56e-01 7.12e+01 ... (remaining 15303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.56: 6612 21.56 - 43.13: 261 43.13 - 64.69: 80 64.69 - 86.25: 10 86.25 - 107.81: 4 Dihedral angle restraints: 6967 sinusoidal: 2919 harmonic: 4048 Sorted by residual: dihedral pdb=" O1B AGS B 402 " pdb=" O3B AGS B 402 " pdb=" PB AGS B 402 " pdb=" PG AGS B 402 " ideal model delta sinusoidal sigma weight residual 68.91 176.72 -107.81 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" CA THR F 35 " pdb=" C THR F 35 " pdb=" N ILE F 36 " pdb=" CA ILE F 36 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA THR F 144 " pdb=" C THR F 144 " pdb=" N SER F 145 " pdb=" CA SER F 145 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 6964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1501 0.082 - 0.163: 160 0.163 - 0.245: 29 0.245 - 0.327: 3 0.327 - 0.409: 2 Chirality restraints: 1695 Sorted by residual: chirality pdb=" CA VAL A 157 " pdb=" N VAL A 157 " pdb=" C VAL A 157 " pdb=" CB VAL A 157 " both_signs ideal model delta sigma weight residual False 2.44 2.85 -0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA VAL A 224 " pdb=" N VAL A 224 " pdb=" C VAL A 224 " pdb=" CB VAL A 224 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CB ILE A 214 " pdb=" CA ILE A 214 " pdb=" CG1 ILE A 214 " pdb=" CG2 ILE A 214 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1692 not shown) Planarity restraints: 1954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 225 " 0.133 2.00e-02 2.50e+03 2.00e-01 3.98e+02 pdb=" C GLU A 225 " -0.345 2.00e-02 2.50e+03 pdb=" O GLU A 225 " 0.110 2.00e-02 2.50e+03 pdb=" N VAL A 226 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 1 " 0.049 2.00e-02 2.50e+03 1.30e-01 1.68e+02 pdb=" C MET F 1 " -0.223 2.00e-02 2.50e+03 pdb=" O MET F 1 " 0.100 2.00e-02 2.50e+03 pdb=" N THR F 2 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 151 " -0.124 5.00e-02 4.00e+02 1.74e-01 4.85e+01 pdb=" N PRO A 152 " 0.301 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " -0.083 5.00e-02 4.00e+02 ... (remaining 1951 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.36: 32 2.36 - 3.01: 6301 3.01 - 3.66: 17259 3.66 - 4.31: 26920 4.31 - 4.96: 44627 Nonbonded interactions: 95139 Sorted by model distance: nonbonded pdb=" NH2 ARG A 671 " pdb=" OD1BASP F 33 " model vdw 1.712 2.520 nonbonded pdb=" OG SER A 151 " pdb=" CD PRO A 152 " model vdw 1.908 3.440 nonbonded pdb="MG MG F 201 " pdb=" O2G GNP F 202 " model vdw 2.027 2.170 nonbonded pdb="MG MG F 201 " pdb=" O2B GNP F 202 " model vdw 2.031 2.170 nonbonded pdb=" OH TYR A 673 " pdb=" OD1BASP F 33 " model vdw 2.062 2.440 ... (remaining 95134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 through 201 or (resid \ 202 and (name N or name CA or name C or name O or name CB )) or resid 203 throug \ h 230)) selection = chain 'D' } 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=0.16 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.650 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: 4.060 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 36.570 Find NCS groups from input model: 0.390 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: 44.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5263 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 : 0.006 0.143 11315 Z= 0.379 Angle : 0.874 38.349 15308 Z= 0.503 Chirality : 0.055 0.409 1695 Planarity : 0.008 0.200 1954 Dihedral : 13.175 107.814 4355 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.76 % Favored : 97.02 % Rotamer: Outliers : 2.90 % Allowed : 6.21 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1359 helix: 0.60 (0.19), residues: 710 sheet: -0.53 (0.42), residues: 137 loop : -1.18 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 216 HIS 0.008 0.001 HIS F 95 PHE 0.033 0.002 PHE A 160 TYR 0.023 0.002 TYR F 96 ARG 0.005 0.001 ARG F 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 461 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 PRO cc_start: 0.7225 (OUTLIER) cc_final: 0.6920 (Cg_exo) REVERT: A 463 ILE cc_start: 0.8379 (mm) cc_final: 0.8008 (mm) REVERT: A 475 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7709 (tptp) REVERT: A 517 MET cc_start: 0.8055 (mmm) cc_final: 0.7784 (mtt) REVERT: A 565 ASP cc_start: 0.7920 (t0) cc_final: 0.7663 (t70) REVERT: A 580 ASN cc_start: 0.8153 (m110) cc_final: 0.7873 (m-40) REVERT: A 721 LEU cc_start: 0.4799 (tp) cc_final: 0.4239 (tp) REVERT: B 146 MET cc_start: 0.4725 (mmm) cc_final: 0.4254 (mmm) REVERT: B 171 ILE cc_start: 0.8110 (mt) cc_final: 0.7830 (mt) REVERT: B 188 HIS cc_start: 0.7378 (t-90) cc_final: 0.6969 (t-90) REVERT: B 236 GLN cc_start: 0.7821 (mt0) cc_final: 0.7482 (tm-30) REVERT: B 253 LEU cc_start: 0.8275 (mt) cc_final: 0.7364 (mt) REVERT: B 329 VAL cc_start: 0.7523 (t) cc_final: 0.7226 (t) REVERT: C 14 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8464 (tm-30) REVERT: C 26 MET cc_start: 0.7632 (tpp) cc_final: 0.7349 (tpp) REVERT: C 83 ARG cc_start: 0.8177 (ttp-170) cc_final: 0.7637 (tmm-80) REVERT: C 96 ASP cc_start: 0.7774 (t70) cc_final: 0.6687 (t0) REVERT: C 98 LEU cc_start: 0.8376 (mt) cc_final: 0.8089 (mm) REVERT: C 118 TYR cc_start: 0.8431 (m-10) cc_final: 0.8172 (m-80) REVERT: C 129 LEU cc_start: 0.9019 (mt) cc_final: 0.8383 (mp) REVERT: C 146 GLN cc_start: 0.9118 (tp40) cc_final: 0.8914 (mm-40) REVERT: C 167 ARG cc_start: 0.7786 (ttt180) cc_final: 0.7265 (ttm170) REVERT: C 177 PHE cc_start: 0.8573 (t80) cc_final: 0.8178 (t80) REVERT: C 218 MET cc_start: 0.8164 (tpp) cc_final: 0.7542 (mmm) REVERT: D 27 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7778 (ttpp) REVERT: D 49 LYS cc_start: 0.7583 (tptm) cc_final: 0.7272 (ttmm) REVERT: D 214 SER cc_start: 0.8010 (p) cc_final: 0.7451 (t) REVERT: F 55 ILE cc_start: 0.3273 (mm) cc_final: 0.3050 (mt) outliers start: 32 outliers final: 6 residues processed: 485 average time/residue: 0.2918 time to fit residues: 186.0079 Evaluate side-chains 266 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 259 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 PRO Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 0.0870 chunk 121 optimal weight: 1.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN A 585 HIS A 628 GLN A 661 ASN B 56 GLN B 87 HIS ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN F 27 HIS F 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5556 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11315 Z= 0.272 Angle : 0.669 7.789 15308 Z= 0.346 Chirality : 0.043 0.207 1695 Planarity : 0.005 0.063 1954 Dihedral : 8.136 98.359 1609 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 3.89 % Allowed : 16.98 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 1359 helix: 1.16 (0.19), residues: 712 sheet: -0.03 (0.42), residues: 140 loop : -1.01 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.014 0.001 HIS A 725 PHE 0.021 0.002 PHE D 153 TYR 0.022 0.002 TYR A 633 ARG 0.010 0.001 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 294 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7677 (tptt) REVERT: A 493 GLN cc_start: 0.8436 (pt0) cc_final: 0.8201 (pm20) REVERT: A 565 ASP cc_start: 0.7980 (t0) cc_final: 0.7742 (t70) REVERT: B 214 GLN cc_start: 0.8272 (mp10) cc_final: 0.7920 (mp10) REVERT: B 219 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7099 (tmm) REVERT: C 12 LEU cc_start: 0.8380 (tp) cc_final: 0.8089 (tp) REVERT: D 49 LYS cc_start: 0.7688 (tptm) cc_final: 0.7293 (ttmm) REVERT: D 160 MET cc_start: 0.3360 (ptp) cc_final: 0.2719 (ptp) REVERT: D 214 SER cc_start: 0.8195 (p) cc_final: 0.7879 (t) REVERT: D 222 ARG cc_start: 0.8310 (mtm110) cc_final: 0.8108 (ttp-110) outliers start: 44 outliers final: 30 residues processed: 320 average time/residue: 0.2465 time to fit residues: 109.2209 Evaluate side-chains 260 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 229 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain F residue 150 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS B 110 GLN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN D 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11315 Z= 0.293 Angle : 0.659 7.462 15308 Z= 0.338 Chirality : 0.044 0.219 1695 Planarity : 0.005 0.078 1954 Dihedral : 8.068 93.759 1606 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.64 % Allowed : 19.55 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.28 (0.23), residues: 1359 helix: 1.09 (0.19), residues: 714 sheet: 0.01 (0.41), residues: 150 loop : -1.03 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 476 HIS 0.011 0.001 HIS A 585 PHE 0.020 0.002 PHE A 707 TYR 0.035 0.002 TYR F 137 ARG 0.007 0.001 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 247 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 LYS cc_start: 0.8075 (mmtt) cc_final: 0.7679 (tptt) REVERT: A 564 MET cc_start: 0.7393 (mmm) cc_final: 0.6522 (tpp) REVERT: A 703 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7113 (tt0) REVERT: B 87 HIS cc_start: 0.6366 (t70) cc_final: 0.5301 (t-90) REVERT: B 111 ILE cc_start: 0.9483 (mt) cc_final: 0.9256 (mm) REVERT: B 122 ASN cc_start: 0.7551 (m-40) cc_final: 0.6095 (p0) REVERT: B 175 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8492 (mtmm) REVERT: B 219 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7218 (tmm) REVERT: B 345 ASN cc_start: 0.7098 (t0) cc_final: 0.6325 (t0) REVERT: C 12 LEU cc_start: 0.8511 (tp) cc_final: 0.8245 (tp) REVERT: C 14 GLU cc_start: 0.9231 (tp30) cc_final: 0.8806 (tp30) REVERT: C 92 GLU cc_start: 0.5300 (tp30) cc_final: 0.5009 (tp30) REVERT: C 178 TYR cc_start: 0.7804 (m-10) cc_final: 0.7551 (m-10) REVERT: D 50 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8558 (t0) REVERT: D 88 LYS cc_start: 0.8405 (tppt) cc_final: 0.7765 (tptp) REVERT: D 118 TYR cc_start: 0.8672 (m-80) cc_final: 0.8368 (m-80) REVERT: D 214 SER cc_start: 0.8136 (p) cc_final: 0.7865 (t) outliers start: 53 outliers final: 33 residues processed: 277 average time/residue: 0.2249 time to fit residues: 89.2790 Evaluate side-chains 261 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 225 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain F residue 108 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 HIS ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN C 67 GLN C 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11315 Z= 0.278 Angle : 0.612 7.639 15308 Z= 0.315 Chirality : 0.043 0.204 1695 Planarity : 0.005 0.071 1954 Dihedral : 7.741 92.400 1604 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.97 % Allowed : 20.63 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.24 (0.23), residues: 1359 helix: 1.08 (0.19), residues: 730 sheet: -0.05 (0.43), residues: 141 loop : -1.14 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 476 HIS 0.007 0.001 HIS B 87 PHE 0.019 0.002 PHE A 707 TYR 0.020 0.002 TYR D 125 ARG 0.009 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 259 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 VAL cc_start: 0.9019 (t) cc_final: 0.8794 (m) REVERT: A 475 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7611 (tptp) REVERT: A 564 MET cc_start: 0.7358 (mmm) cc_final: 0.6535 (tpp) REVERT: B 111 ILE cc_start: 0.9450 (mt) cc_final: 0.9162 (mm) REVERT: B 122 ASN cc_start: 0.7575 (m-40) cc_final: 0.6130 (p0) REVERT: B 175 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8551 (mtmm) REVERT: B 219 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7339 (tmm) REVERT: B 274 MET cc_start: 0.7993 (mtp) cc_final: 0.7776 (mtp) REVERT: C 12 LEU cc_start: 0.8599 (tp) cc_final: 0.8324 (tp) REVERT: C 14 GLU cc_start: 0.9263 (tp30) cc_final: 0.8900 (tm-30) REVERT: C 92 GLU cc_start: 0.5394 (tp30) cc_final: 0.5102 (tp30) REVERT: C 178 TYR cc_start: 0.7847 (m-10) cc_final: 0.7620 (m-10) REVERT: D 88 LYS cc_start: 0.8451 (tppt) cc_final: 0.7835 (tptp) REVERT: D 118 TYR cc_start: 0.8641 (m-80) cc_final: 0.8258 (m-80) REVERT: D 214 SER cc_start: 0.8169 (p) cc_final: 0.7868 (t) REVERT: F 93 ILE cc_start: 0.5394 (mt) cc_final: 0.4852 (mt) REVERT: F 159 LEU cc_start: 0.3593 (tp) cc_final: 0.2880 (tp) outliers start: 55 outliers final: 34 residues processed: 291 average time/residue: 0.2192 time to fit residues: 91.7456 Evaluate side-chains 265 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 229 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 506 ARG Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain F residue 108 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 568 HIS ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 11315 Z= 0.505 Angle : 0.838 13.522 15308 Z= 0.421 Chirality : 0.049 0.294 1695 Planarity : 0.006 0.072 1954 Dihedral : 7.928 88.391 1603 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 6.38 % Allowed : 21.04 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.28 (0.23), residues: 1359 helix: 0.54 (0.19), residues: 726 sheet: -0.17 (0.44), residues: 134 loop : -1.17 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 476 HIS 0.012 0.002 HIS A 269 PHE 0.023 0.003 PHE A 707 TYR 0.023 0.003 TYR C 125 ARG 0.008 0.001 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 246 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7226 (ttm) cc_final: 0.6968 (tpp) REVERT: A 471 VAL cc_start: 0.9260 (t) cc_final: 0.9047 (p) REVERT: A 475 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7741 (tptt) REVERT: A 585 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6534 (m90) REVERT: A 650 MET cc_start: 0.7540 (tpp) cc_final: 0.6908 (mmt) REVERT: A 734 ASN cc_start: 0.7687 (t0) cc_final: 0.7477 (p0) REVERT: B 102 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7413 (pt0) REVERT: B 143 MET cc_start: 0.5104 (OUTLIER) cc_final: 0.4585 (mtp) REVERT: B 175 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8586 (mtmm) REVERT: B 219 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7498 (tmm) REVERT: B 251 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8014 (tt) REVERT: B 255 GLU cc_start: 0.7736 (tp30) cc_final: 0.6330 (tp30) REVERT: C 12 LEU cc_start: 0.8877 (tp) cc_final: 0.8583 (tp) REVERT: C 111 ASN cc_start: 0.8536 (m-40) cc_final: 0.8160 (m110) REVERT: C 164 HIS cc_start: 0.8433 (t-90) cc_final: 0.7740 (t70) REVERT: D 40 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8025 (mm-30) REVERT: D 46 VAL cc_start: 0.9317 (p) cc_final: 0.9004 (t) REVERT: D 88 LYS cc_start: 0.8624 (tppt) cc_final: 0.7766 (tmtt) REVERT: D 118 TYR cc_start: 0.8637 (m-80) cc_final: 0.8393 (m-80) REVERT: D 121 MET cc_start: 0.7939 (ttm) cc_final: 0.7378 (tpp) REVERT: D 214 SER cc_start: 0.8095 (p) cc_final: 0.7861 (t) outliers start: 72 outliers final: 47 residues processed: 296 average time/residue: 0.2195 time to fit residues: 93.3422 Evaluate side-chains 271 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 218 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 108 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 129 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 0.0870 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN C 42 ASN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 11315 Z= 0.226 Angle : 0.661 12.660 15308 Z= 0.334 Chirality : 0.044 0.309 1695 Planarity : 0.005 0.074 1954 Dihedral : 7.706 87.038 1599 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.39 % Allowed : 24.36 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 1359 helix: 0.89 (0.19), residues: 735 sheet: -0.17 (0.45), residues: 133 loop : -1.14 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 476 HIS 0.035 0.002 HIS A 269 PHE 0.015 0.002 PHE A 707 TYR 0.022 0.002 TYR C 125 ARG 0.008 0.000 ARG F 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 247 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7175 (ttm) cc_final: 0.6925 (tpp) REVERT: A 475 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7631 (tptt) REVERT: A 564 MET cc_start: 0.7171 (mmm) cc_final: 0.6792 (mmm) REVERT: A 585 HIS cc_start: 0.6930 (OUTLIER) cc_final: 0.6603 (m90) REVERT: A 627 MET cc_start: 0.8869 (tpp) cc_final: 0.8614 (tpp) REVERT: B 81 VAL cc_start: 0.8491 (t) cc_final: 0.8259 (t) REVERT: B 143 MET cc_start: 0.4958 (OUTLIER) cc_final: 0.4581 (mtp) REVERT: B 175 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8578 (mtmm) REVERT: B 219 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7467 (tmm) REVERT: C 12 LEU cc_start: 0.8710 (tp) cc_final: 0.8446 (tp) REVERT: C 14 GLU cc_start: 0.9328 (tp30) cc_final: 0.8425 (tp30) REVERT: C 111 ASN cc_start: 0.8488 (m-40) cc_final: 0.8115 (m110) REVERT: C 160 MET cc_start: 0.7315 (tpp) cc_final: 0.7026 (tpp) REVERT: C 164 HIS cc_start: 0.8321 (t-90) cc_final: 0.7953 (t-90) REVERT: D 88 LYS cc_start: 0.8348 (tppt) cc_final: 0.7677 (tptp) REVERT: D 118 TYR cc_start: 0.8522 (m-80) cc_final: 0.8293 (m-80) REVERT: D 121 MET cc_start: 0.7849 (ttm) cc_final: 0.7301 (tpp) REVERT: D 214 SER cc_start: 0.8124 (p) cc_final: 0.7837 (t) REVERT: F 55 ILE cc_start: 0.4115 (mm) cc_final: 0.3610 (mt) outliers start: 48 outliers final: 36 residues processed: 279 average time/residue: 0.2226 time to fit residues: 88.9384 Evaluate side-chains 265 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 225 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 129 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5805 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11315 Z= 0.229 Angle : 0.653 15.937 15308 Z= 0.327 Chirality : 0.044 0.358 1695 Planarity : 0.004 0.065 1954 Dihedral : 7.628 84.185 1599 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.06 % Allowed : 25.68 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 1359 helix: 1.07 (0.19), residues: 731 sheet: -0.08 (0.46), residues: 133 loop : -1.09 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 476 HIS 0.021 0.001 HIS A 269 PHE 0.020 0.002 PHE A 160 TYR 0.018 0.002 TYR C 125 ARG 0.010 0.001 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 238 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7165 (ttm) cc_final: 0.6910 (tpp) REVERT: A 475 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7618 (tptt) REVERT: A 571 SER cc_start: 0.8722 (m) cc_final: 0.8455 (t) REVERT: A 585 HIS cc_start: 0.6996 (OUTLIER) cc_final: 0.6649 (m90) REVERT: A 650 MET cc_start: 0.7501 (tpp) cc_final: 0.6992 (mmt) REVERT: B 81 VAL cc_start: 0.8532 (t) cc_final: 0.8274 (t) REVERT: B 219 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7443 (tmm) REVERT: B 316 TYR cc_start: 0.6990 (t80) cc_final: 0.6760 (t80) REVERT: C 12 LEU cc_start: 0.8733 (tp) cc_final: 0.8442 (tp) REVERT: C 14 GLU cc_start: 0.9341 (tp30) cc_final: 0.8518 (tp30) REVERT: C 111 ASN cc_start: 0.8427 (m-40) cc_final: 0.8019 (m110) REVERT: C 164 HIS cc_start: 0.8280 (t-90) cc_final: 0.7861 (t70) REVERT: D 40 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8006 (mt-10) REVERT: D 88 LYS cc_start: 0.8358 (tppt) cc_final: 0.7714 (tptp) REVERT: D 118 TYR cc_start: 0.8497 (m-80) cc_final: 0.8271 (m-80) REVERT: D 214 SER cc_start: 0.8164 (p) cc_final: 0.7866 (t) REVERT: F 55 ILE cc_start: 0.4490 (mm) cc_final: 0.4055 (mt) outliers start: 45 outliers final: 35 residues processed: 267 average time/residue: 0.2199 time to fit residues: 84.0557 Evaluate side-chains 258 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 221 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain F residue 108 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 112 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 HIS ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.6984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 11315 Z= 0.471 Angle : 0.820 13.517 15308 Z= 0.409 Chirality : 0.049 0.371 1695 Planarity : 0.005 0.067 1954 Dihedral : 7.903 82.812 1599 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.05 % Allowed : 25.60 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -0.08 (0.23), residues: 1359 helix: 0.71 (0.19), residues: 717 sheet: 0.27 (0.47), residues: 124 loop : -1.17 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 476 HIS 0.019 0.002 HIS A 269 PHE 0.023 0.003 PHE A 707 TYR 0.024 0.002 TYR C 125 ARG 0.008 0.001 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 222 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TRP cc_start: 0.6195 (m100) cc_final: 0.5558 (m100) REVERT: A 475 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7602 (tptt) REVERT: A 585 HIS cc_start: 0.7084 (OUTLIER) cc_final: 0.6777 (m90) REVERT: A 623 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6075 (mm-30) REVERT: B 143 MET cc_start: 0.5146 (OUTLIER) cc_final: 0.3944 (mtp) REVERT: B 219 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7482 (tmm) REVERT: B 227 ARG cc_start: 0.9327 (ptp90) cc_final: 0.9063 (ptp90) REVERT: B 356 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7080 (mtt) REVERT: C 12 LEU cc_start: 0.8787 (tp) cc_final: 0.8548 (tp) REVERT: C 73 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.6320 (pm20) REVERT: C 111 ASN cc_start: 0.8434 (m-40) cc_final: 0.8012 (m110) REVERT: C 164 HIS cc_start: 0.8406 (t-90) cc_final: 0.7893 (t70) REVERT: D 88 LYS cc_start: 0.8488 (tppt) cc_final: 0.7845 (tptp) REVERT: D 118 TYR cc_start: 0.8620 (m-80) cc_final: 0.8399 (m-80) REVERT: D 121 MET cc_start: 0.7945 (ttm) cc_final: 0.7521 (tpp) REVERT: D 206 LEU cc_start: 0.5489 (OUTLIER) cc_final: 0.5178 (mt) REVERT: D 214 SER cc_start: 0.8121 (p) cc_final: 0.7796 (t) REVERT: F 159 LEU cc_start: 0.3352 (tp) cc_final: 0.3026 (tp) outliers start: 57 outliers final: 45 residues processed: 258 average time/residue: 0.2140 time to fit residues: 79.8467 Evaluate side-chains 261 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 210 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 239 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 108 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.7029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11315 Z= 0.241 Angle : 0.697 14.187 15308 Z= 0.350 Chirality : 0.044 0.286 1695 Planarity : 0.004 0.069 1954 Dihedral : 7.930 81.157 1599 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.81 % Allowed : 27.42 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 0.22 (0.23), residues: 1359 helix: 1.02 (0.19), residues: 716 sheet: 0.28 (0.47), residues: 127 loop : -1.10 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 450 HIS 0.016 0.001 HIS A 269 PHE 0.020 0.002 PHE A 250 TYR 0.025 0.002 TYR B 316 ARG 0.013 0.001 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 237 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 THR cc_start: 0.7834 (m) cc_final: 0.7114 (p) REVERT: A 475 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7572 (tptt) REVERT: A 585 HIS cc_start: 0.7125 (OUTLIER) cc_final: 0.6837 (m90) REVERT: A 650 MET cc_start: 0.7419 (tpp) cc_final: 0.6896 (mmt) REVERT: B 219 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7444 (tmm) REVERT: B 356 MET cc_start: 0.7588 (ptp) cc_final: 0.7009 (mtt) REVERT: C 12 LEU cc_start: 0.8678 (tp) cc_final: 0.8431 (tp) REVERT: C 14 GLU cc_start: 0.9279 (tp30) cc_final: 0.8522 (tp30) REVERT: C 111 ASN cc_start: 0.8460 (m-40) cc_final: 0.8050 (m110) REVERT: C 164 HIS cc_start: 0.8333 (t-90) cc_final: 0.7853 (t70) REVERT: D 88 LYS cc_start: 0.8397 (tppt) cc_final: 0.7749 (tptp) REVERT: D 121 MET cc_start: 0.7797 (ttm) cc_final: 0.7374 (tpp) REVERT: D 214 SER cc_start: 0.8012 (p) cc_final: 0.7651 (t) REVERT: F 159 LEU cc_start: 0.3346 (tp) cc_final: 0.3113 (tp) outliers start: 42 outliers final: 32 residues processed: 267 average time/residue: 0.2434 time to fit residues: 95.0692 Evaluate side-chains 253 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 219 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain F residue 108 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 133 optimal weight: 30.0000 chunk 122 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 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 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.7331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11315 Z= 0.400 Angle : 0.794 13.161 15308 Z= 0.399 Chirality : 0.048 0.343 1695 Planarity : 0.005 0.070 1954 Dihedral : 8.032 78.076 1599 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.81 % Allowed : 27.59 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 0.09 (0.23), residues: 1359 helix: 0.82 (0.19), residues: 718 sheet: 0.34 (0.46), residues: 132 loop : -1.05 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 450 HIS 0.014 0.002 HIS A 269 PHE 0.023 0.002 PHE A 707 TYR 0.037 0.002 TYR D 118 ARG 0.013 0.001 ARG D 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 222 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7534 (tptt) REVERT: A 585 HIS cc_start: 0.7138 (OUTLIER) cc_final: 0.6837 (m90) REVERT: A 623 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6104 (mm-30) REVERT: A 701 ARG cc_start: 0.7851 (ptm-80) cc_final: 0.7350 (ptp-170) REVERT: B 101 LEU cc_start: 0.7610 (mt) cc_final: 0.7371 (tp) REVERT: B 219 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7449 (tmm) REVERT: B 356 MET cc_start: 0.7631 (ptp) cc_final: 0.7036 (mtt) REVERT: C 14 GLU cc_start: 0.9331 (tp30) cc_final: 0.8392 (tp30) REVERT: C 81 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8079 (pp20) REVERT: C 111 ASN cc_start: 0.8481 (m-40) cc_final: 0.8027 (m110) REVERT: C 164 HIS cc_start: 0.8242 (t-90) cc_final: 0.7840 (t-90) REVERT: D 88 LYS cc_start: 0.8201 (tppt) cc_final: 0.7607 (tptp) REVERT: D 121 MET cc_start: 0.7901 (ttm) cc_final: 0.7482 (tpp) REVERT: D 214 SER cc_start: 0.8060 (p) cc_final: 0.7764 (t) REVERT: D 215 THR cc_start: 0.8147 (p) cc_final: 0.7695 (t) REVERT: F 159 LEU cc_start: 0.3455 (tp) cc_final: 0.3210 (tp) outliers start: 42 outliers final: 36 residues processed: 253 average time/residue: 0.2219 time to fit residues: 81.1639 Evaluate side-chains 254 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 215 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 26 MET Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 108 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 106 optimal weight: 0.0040 chunk 44 optimal weight: 20.0000 chunk 109 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN C 42 ASN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.209399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.173837 restraints weight = 59644.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.175355 restraints weight = 31142.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.173698 restraints weight = 13970.550| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.7377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11315 Z= 0.212 Angle : 0.705 14.383 15308 Z= 0.355 Chirality : 0.044 0.341 1695 Planarity : 0.005 0.069 1954 Dihedral : 8.026 77.192 1599 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.15 % Allowed : 28.75 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.08 % 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: 1359 helix: 1.02 (0.19), residues: 720 sheet: 0.29 (0.48), residues: 118 loop : -0.99 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 476 HIS 0.016 0.001 HIS A 269 PHE 0.024 0.002 PHE A 250 TYR 0.027 0.002 TYR D 118 ARG 0.015 0.001 ARG D 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2506.17 seconds wall clock time: 46 minutes 32.14 seconds (2792.14 seconds total)