Starting phenix.real_space_refine on Sat Feb 17 03:45:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd7_4808/02_2024/6rd7_4808.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd7_4808/02_2024/6rd7_4808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd7_4808/02_2024/6rd7_4808.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd7_4808/02_2024/6rd7_4808.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd7_4808/02_2024/6rd7_4808.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd7_4808/02_2024/6rd7_4808.pdb" } resolution = 2.73 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 58 5.16 5 C 11231 2.51 5 N 2862 2.21 5 O 3254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 58": "OE1" <-> "OE2" Residue "1 ASP 69": "OD1" <-> "OD2" Residue "1 ARG 90": "NH1" <-> "NH2" Residue "1 ASP 96": "OD1" <-> "OD2" Residue "1 ARG 118": "NH1" <-> "NH2" Residue "1 GLU 138": "OE1" <-> "OE2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 223": "OE1" <-> "OE2" Residue "1 ARG 252": "NH1" <-> "NH2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 GLU 341": "OE1" <-> "OE2" Residue "1 ASP 353": "OD1" <-> "OD2" Residue "1 GLU 355": "OE1" <-> "OE2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 GLU 385": "OE1" <-> "OE2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 425": "OD1" <-> "OD2" Residue "1 PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 ASP 442": "OD1" <-> "OD2" Residue "1 GLU 452": "OE1" <-> "OE2" Residue "1 GLU 457": "OE1" <-> "OE2" Residue "1 ASP 479": "OD1" <-> "OD2" Residue "1 ASP 486": "OD1" <-> "OD2" Residue "1 GLU 499": "OE1" <-> "OE2" Residue "1 GLU 501": "OE1" <-> "OE2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 GLU 519": "OE1" <-> "OE2" Residue "1 GLU 559": "OE1" <-> "OE2" Residue "1 GLU 577": "OE1" <-> "OE2" Residue "1 ARG 597": "NH1" <-> "NH2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "1 ASP 613": "OD1" <-> "OD2" Residue "3 ASP 102": "OD1" <-> "OD2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 276": "OE1" <-> "OE2" Residue "3 GLU 279": "OE1" <-> "OE2" Residue "3 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 299": "OE1" <-> "OE2" Residue "3 GLU 308": "OE1" <-> "OE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 104": "OD1" <-> "OD2" Residue "5 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 89": "NH1" <-> "NH2" Residue "6 ASP 91": "OD1" <-> "OD2" Residue "6 ARG 130": "NH1" <-> "NH2" Residue "6 PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 5": "OE1" <-> "OE2" Residue "8 ARG 13": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "8 TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 12": "OE1" <-> "OE2" Residue "9 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 17": "OD1" <-> "OD2" Residue "9 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "I GLU 111": "OE1" <-> "OE2" Residue "J ARG 91": "NH1" <-> "NH2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "M PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 313": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17406 Number of models: 1 Model: "" Number of chains: 26 Chain: "0" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 605 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Unusual residues: {' ZN': 1} Classifications: {'peptide': 217, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204, None: 1} Not linked: pdbres="LYS M 324 " pdbres=" ZN M 600 " Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "1" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "5" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "6" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "8" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 9.54, per 1000 atoms: 0.55 Number of scatterers: 17406 At special positions: 0 Unit cell: (129.519, 117.936, 221.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 58 16.00 O 3254 8.00 N 2862 7.00 C 11231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 9 69 " - pdb=" SG CYS 9 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.17 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 2 sheets defined 79.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain '0' and resid 3 through 10 removed outlier: 3.876A pdb=" N ALA 0 10 " --> pdb=" O TYR 0 6 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 31 removed outlier: 3.666A pdb=" N ALA 0 27 " --> pdb=" O ALA 0 23 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 Processing helix chain '0' and resid 57 through 61 Processing helix chain '1' and resid 46 through 74 Processing helix chain '1' and resid 83 through 87 Processing helix chain '1' and resid 106 through 143 removed outlier: 3.866A pdb=" N LYS 1 143 " --> pdb=" O ALA 1 139 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 177 Processing helix chain '1' and resid 190 through 205 Processing helix chain '1' and resid 209 through 224 removed outlier: 3.835A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 271 Processing helix chain '1' and resid 272 through 277 removed outlier: 3.511A pdb=" N VAL 1 277 " --> pdb=" O LEU 1 274 " (cutoff:3.500A) Processing helix chain '1' and resid 281 through 285 Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 Processing helix chain '1' and resid 310 through 317 Processing helix chain '1' and resid 318 through 322 Processing helix chain '1' and resid 323 through 327 removed outlier: 3.663A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 351 Processing helix chain '1' and resid 353 through 363 Processing helix chain '1' and resid 364 through 367 removed outlier: 3.831A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 364 through 367' Processing helix chain '1' and resid 375 through 388 Processing helix chain '1' and resid 392 through 421 removed outlier: 3.583A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY 1 421 " --> pdb=" O LYS 1 417 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.607A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 446 removed outlier: 3.661A pdb=" N ASN 1 446 " --> pdb=" O ASP 1 442 " (cutoff:3.500A) Processing helix chain '1' and resid 446 through 461 Processing helix chain '1' and resid 463 through 479 removed outlier: 3.930A pdb=" N ASP 1 479 " --> pdb=" O GLU 1 475 " (cutoff:3.500A) Processing helix chain '1' and resid 480 through 483 Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 516 removed outlier: 3.538A pdb=" N GLU 1 516 " --> pdb=" O LEU 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.635A pdb=" N LEU 1 522 " --> pdb=" O GLU 1 518 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 Processing helix chain '1' and resid 549 through 562 Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 Processing helix chain '1' and resid 610 through 614 Processing helix chain '3' and resid 78 through 90 Processing helix chain '3' and resid 93 through 98 Processing helix chain '3' and resid 102 through 112 Processing helix chain '3' and resid 117 through 129 removed outlier: 4.211A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 135 Processing helix chain '3' and resid 136 through 151 Processing helix chain '3' and resid 154 through 168 Processing helix chain '3' and resid 173 through 187 removed outlier: 4.080A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE 3 187 " --> pdb=" O THR 3 183 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 204 Processing helix chain '3' and resid 215 through 229 Processing helix chain '3' and resid 233 through 242 Processing helix chain '3' and resid 245 through 251 Processing helix chain '3' and resid 253 through 272 removed outlier: 3.636A pdb=" N ASP 3 259 " --> pdb=" O ALA 3 255 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 287 removed outlier: 3.605A pdb=" N VAL 3 281 " --> pdb=" O SER 3 277 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 312 Processing helix chain '5' and resid 7 through 29 removed outlier: 3.537A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 29 through 59 removed outlier: 4.036A pdb=" N THR 5 33 " --> pdb=" O GLN 5 29 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 68 Processing helix chain '5' and resid 72 through 81 removed outlier: 3.683A pdb=" N VAL 5 76 " --> pdb=" O SER 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 87 through 107 removed outlier: 4.336A pdb=" N HIS 5 91 " --> pdb=" O ALA 5 87 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 Processing helix chain '6' and resid 30 through 42 removed outlier: 3.610A pdb=" N THR 6 42 " --> pdb=" O SER 6 38 " (cutoff:3.500A) Processing helix chain '6' and resid 46 through 59 removed outlier: 5.041A pdb=" N LYS 6 52 " --> pdb=" O LEU 6 48 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR 6 53 " --> pdb=" O SER 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 72 through 95 Processing helix chain '6' and resid 98 through 120 removed outlier: 3.658A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 131 Processing helix chain '6' and resid 133 through 138 removed outlier: 3.841A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '8' and resid 4 through 9 removed outlier: 3.717A pdb=" N LYS 8 9 " --> pdb=" O VAL 8 6 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 31 Processing helix chain '8' and resid 31 through 39 removed outlier: 3.557A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 79 removed outlier: 6.881A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 16 Processing helix chain '9' and resid 19 through 24 Processing helix chain '9' and resid 33 through 55 Processing helix chain '9' and resid 76 through 80 Processing helix chain '9' and resid 82 through 96 removed outlier: 4.014A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 70 through 92 Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.826A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 70 through 92 Processing helix chain 'B' and resid 95 through 126 removed outlier: 3.825A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 Processing helix chain 'C' and resid 70 through 92 Processing helix chain 'C' and resid 95 through 126 removed outlier: 3.826A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 70 through 92 Processing helix chain 'D' and resid 95 through 126 removed outlier: 3.827A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'E' and resid 70 through 92 Processing helix chain 'E' and resid 95 through 126 removed outlier: 3.826A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 Processing helix chain 'F' and resid 70 through 92 Processing helix chain 'F' and resid 95 through 126 removed outlier: 3.826A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.609A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 92 Processing helix chain 'G' and resid 95 through 126 removed outlier: 3.827A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 Processing helix chain 'H' and resid 70 through 92 Processing helix chain 'H' and resid 95 through 126 removed outlier: 3.827A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 Processing helix chain 'I' and resid 70 through 92 Processing helix chain 'I' and resid 95 through 126 removed outlier: 3.826A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 Processing helix chain 'J' and resid 70 through 92 Processing helix chain 'J' and resid 95 through 126 removed outlier: 3.826A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 119 Processing helix chain 'M' and resid 134 through 145 Processing helix chain 'M' and resid 147 through 166 removed outlier: 3.638A pdb=" N CYS M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY M 166 " --> pdb=" O CYS M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 201 removed outlier: 3.637A pdb=" N ALA M 181 " --> pdb=" O GLY M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 266 removed outlier: 3.964A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN M 243 " --> pdb=" O ARG M 239 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 270 through 308 removed outlier: 3.771A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 311 No H-bonds generated for 'chain 'M' and resid 309 through 311' Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 185 removed outlier: 3.629A pdb=" N LYS 1 183 " --> pdb=" O THR 1 228 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL 1 226 " --> pdb=" O ALA 1 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '3' and resid 314 through 317 1337 hydrogen bonds defined for protein. 3933 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: 4.99 Time building geometry restraints manager: 7.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3486 1.33 - 1.45: 3911 1.45 - 1.57: 10140 1.57 - 1.69: 1 1.69 - 1.81: 97 Bond restraints: 17635 Sorted by residual: bond pdb=" C VAL 3 103 " pdb=" N PRO 3 104 " ideal model delta sigma weight residual 1.335 1.403 -0.068 1.30e-02 5.92e+03 2.74e+01 bond pdb=" C VAL M 222 " pdb=" N PRO M 223 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.36e-02 5.41e+03 2.35e+01 bond pdb=" N THR 9 76 " pdb=" CA THR 9 76 " ideal model delta sigma weight residual 1.454 1.492 -0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" N CYS 9 69 " pdb=" CA CYS 9 69 " ideal model delta sigma weight residual 1.455 1.485 -0.031 9.60e-03 1.09e+04 1.01e+01 bond pdb=" C LEU 5 31 " pdb=" N PRO 5 32 " ideal model delta sigma weight residual 1.335 1.375 -0.040 1.36e-02 5.41e+03 8.60e+00 ... (remaining 17630 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.13: 391 106.13 - 113.28: 9898 113.28 - 120.43: 7108 120.43 - 127.58: 6389 127.58 - 134.73: 145 Bond angle restraints: 23931 Sorted by residual: angle pdb=" N PRO 3 77 " pdb=" CA PRO 3 77 " pdb=" CB PRO 3 77 " ideal model delta sigma weight residual 103.00 110.37 -7.37 1.10e+00 8.26e-01 4.48e+01 angle pdb=" C ASP 1 106 " pdb=" N VAL 1 107 " pdb=" CA VAL 1 107 " ideal model delta sigma weight residual 120.24 124.41 -4.17 6.30e-01 2.52e+00 4.38e+01 angle pdb=" C ASP 1 91 " pdb=" N TYR 1 92 " pdb=" CA TYR 1 92 " ideal model delta sigma weight residual 120.67 129.25 -8.58 1.34e+00 5.57e-01 4.10e+01 angle pdb=" C VAL 5 71 " pdb=" N SER 5 72 " pdb=" CA SER 5 72 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 angle pdb=" N VAL 1 204 " pdb=" CA VAL 1 204 " pdb=" C VAL 1 204 " ideal model delta sigma weight residual 110.62 105.74 4.88 1.02e+00 9.61e-01 2.29e+01 ... (remaining 23926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9492 17.70 - 35.40: 787 35.40 - 53.11: 109 53.11 - 70.81: 35 70.81 - 88.51: 11 Dihedral angle restraints: 10434 sinusoidal: 3836 harmonic: 6598 Sorted by residual: dihedral pdb=" CB CYS 9 69 " pdb=" SG CYS 9 69 " pdb=" SG CYS 9 79 " pdb=" CB CYS 9 79 " ideal model delta sinusoidal sigma weight residual 93.00 178.33 -85.33 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CA LYS M 203 " pdb=" C LYS M 203 " pdb=" N PHE M 204 " pdb=" CA PHE M 204 " ideal model delta harmonic sigma weight residual -180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA VAL 5 71 " pdb=" C VAL 5 71 " pdb=" N SER 5 72 " pdb=" CA SER 5 72 " ideal model delta harmonic sigma weight residual 180.00 153.39 26.61 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 10431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2086 0.050 - 0.100: 584 0.100 - 0.149: 139 0.149 - 0.199: 15 0.199 - 0.249: 5 Chirality restraints: 2829 Sorted by residual: chirality pdb=" CA VAL 1 204 " pdb=" N VAL 1 204 " pdb=" C VAL 1 204 " pdb=" CB VAL 1 204 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA PRO 3 77 " pdb=" N PRO 3 77 " pdb=" C PRO 3 77 " pdb=" CB PRO 3 77 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CG LEU 1 102 " pdb=" CB LEU 1 102 " pdb=" CD1 LEU 1 102 " pdb=" CD2 LEU 1 102 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2826 not shown) Planarity restraints: 3016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY 9 67 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C GLY 9 67 " 0.062 2.00e-02 2.50e+03 pdb=" O GLY 9 67 " -0.024 2.00e-02 2.50e+03 pdb=" N MET 9 68 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 108 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C ALA G 108 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA G 108 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU G 109 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 108 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.87e+00 pdb=" C ALA C 108 " 0.049 2.00e-02 2.50e+03 pdb=" O ALA C 108 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU C 109 " -0.016 2.00e-02 2.50e+03 ... (remaining 3013 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 117 2.50 - 3.10: 12472 3.10 - 3.70: 28318 3.70 - 4.30: 41456 4.30 - 4.90: 66132 Nonbonded interactions: 148495 Sorted by model distance: nonbonded pdb=" O ALA E 58 " pdb=" OG SER F 59 " model vdw 1.905 2.440 nonbonded pdb=" CG ARG 1 28 " pdb=" OD1 ASP 1 30 " model vdw 2.017 3.440 nonbonded pdb=" OE2 GLU H 111 " pdb=" CD1 ILE I 113 " model vdw 2.042 3.460 nonbonded pdb=" OE2 GLU F 111 " pdb=" CD1 ILE G 113 " model vdw 2.115 3.460 nonbonded pdb=" OE2 GLU I 111 " pdb=" CD1 ILE J 113 " model vdw 2.139 3.460 ... (remaining 148490 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.800 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: 25.300 Check model and map are aligned: 0.300 Set scattering table: 0.150 Process input model: 50.020 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 0.068 17635 Z= 0.411 Angle : 0.894 11.847 23931 Z= 0.545 Chirality : 0.049 0.249 2829 Planarity : 0.009 0.063 3016 Dihedral : 13.556 88.511 6183 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.50 % Favored : 98.28 % Rotamer: Outliers : 0.84 % Allowed : 4.88 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 2271 helix: -0.98 (0.11), residues: 1724 sheet: None (None), residues: 0 loop : -1.58 (0.22), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 9 73 HIS 0.012 0.001 HIS M 252 PHE 0.034 0.002 PHE M 231 TYR 0.032 0.002 TYR 3 153 ARG 0.004 0.000 ARG 1 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 405 time to evaluate : 2.058 Fit side-chains REVERT: 0 34 ARG cc_start: 0.8056 (ptt-90) cc_final: 0.7765 (ptt-90) REVERT: 0 41 GLU cc_start: 0.5947 (pp20) cc_final: 0.5706 (pp20) REVERT: 0 44 ASN cc_start: 0.8678 (m110) cc_final: 0.8240 (m-40) REVERT: 0 60 GLN cc_start: 0.8925 (mm110) cc_final: 0.8705 (mm-40) REVERT: 1 224 LYS cc_start: 0.8422 (mtmm) cc_final: 0.7487 (pptt) REVERT: 1 387 ARG cc_start: 0.7989 (mtp180) cc_final: 0.7512 (mtm-85) REVERT: 1 441 PHE cc_start: 0.8364 (m-80) cc_final: 0.8134 (m-80) REVERT: 1 613 ASP cc_start: 0.8183 (m-30) cc_final: 0.7864 (m-30) REVERT: 3 82 VAL cc_start: 0.3772 (OUTLIER) cc_final: 0.3533 (t) REVERT: 3 151 ASN cc_start: 0.7735 (t0) cc_final: 0.7522 (t160) REVERT: 5 6 GLU cc_start: 0.7817 (tt0) cc_final: 0.7574 (tt0) REVERT: 5 109 GLN cc_start: 0.8595 (mp-120) cc_final: 0.8311 (mm-40) REVERT: 6 86 ILE cc_start: 0.8978 (mt) cc_final: 0.8696 (mm) REVERT: 9 9 LYS cc_start: 0.7264 (ttpt) cc_final: 0.6754 (ttpp) REVERT: 9 68 MET cc_start: 0.7984 (mtm) cc_final: 0.7726 (mtm) REVERT: 9 95 LYS cc_start: 0.7781 (mmtm) cc_final: 0.7571 (mmtp) REVERT: D 92 ASN cc_start: 0.7955 (t0) cc_final: 0.7748 (t0) REVERT: F 81 MET cc_start: 0.8340 (ttp) cc_final: 0.7920 (ttm) REVERT: G 81 MET cc_start: 0.8172 (ttp) cc_final: 0.7826 (ttp) REVERT: G 115 LEU cc_start: 0.7468 (mt) cc_final: 0.7257 (pp) REVERT: H 81 MET cc_start: 0.8582 (ttp) cc_final: 0.8305 (ttp) REVERT: H 102 TYR cc_start: 0.7382 (m-10) cc_final: 0.7134 (m-10) REVERT: I 92 ASN cc_start: 0.8507 (t0) cc_final: 0.8288 (t0) REVERT: I 102 TYR cc_start: 0.7582 (m-10) cc_final: 0.7283 (m-10) REVERT: M 225 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7330 (mm-30) outliers start: 15 outliers final: 5 residues processed: 419 average time/residue: 1.0903 time to fit residues: 518.3945 Evaluate side-chains 287 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 281 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 203 SER Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 3 residue 82 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain J residue 80 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 0.0970 chunk 169 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 114 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 chunk 130 optimal weight: 0.3980 chunk 202 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 1 100 GLN 1 316 ASN 1 428 HIS 1 482 ASN ** 1 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 527 GLN 1 562 ASN ** 3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 206 ASN 3 269 GLN 5 29 GLN 6 40 ASN 8 26 HIS 8 29 GLN 9 35 GLN ** 9 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 60 ASN G 98 GLN J 87 ASN J 98 GLN M 108 ASN M 163 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17635 Z= 0.176 Angle : 0.508 7.147 23931 Z= 0.267 Chirality : 0.036 0.139 2829 Planarity : 0.004 0.050 3016 Dihedral : 4.536 29.237 2417 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.28 % Favored : 98.68 % Rotamer: Outliers : 2.58 % Allowed : 12.86 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2271 helix: 0.72 (0.12), residues: 1744 sheet: None (None), residues: 0 loop : -0.66 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 583 HIS 0.011 0.001 HIS 1 428 PHE 0.018 0.001 PHE D 116 TYR 0.015 0.001 TYR 5 51 ARG 0.007 0.000 ARG 1 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 314 time to evaluate : 2.328 Fit side-chains REVERT: 0 34 ARG cc_start: 0.7949 (ptt-90) cc_final: 0.7336 (ptt-90) REVERT: 0 44 ASN cc_start: 0.8679 (m110) cc_final: 0.8346 (m-40) REVERT: 1 224 LYS cc_start: 0.8403 (mtmm) cc_final: 0.7443 (pptt) REVERT: 1 387 ARG cc_start: 0.7892 (mtp180) cc_final: 0.7530 (mtm-85) REVERT: 1 441 PHE cc_start: 0.8048 (m-80) cc_final: 0.7804 (m-80) REVERT: 1 452 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7364 (tm-30) REVERT: 1 501 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7294 (mm-30) REVERT: 3 151 ASN cc_start: 0.7904 (t0) cc_final: 0.7687 (t0) REVERT: 5 6 GLU cc_start: 0.7855 (tt0) cc_final: 0.7320 (tt0) REVERT: 6 86 ILE cc_start: 0.8948 (mt) cc_final: 0.8636 (mm) REVERT: 9 9 LYS cc_start: 0.7087 (ttpt) cc_final: 0.6480 (ttpp) REVERT: 9 12 GLU cc_start: 0.8223 (tt0) cc_final: 0.7940 (tt0) REVERT: 9 95 LYS cc_start: 0.7808 (mmtm) cc_final: 0.7546 (mmtp) REVERT: D 119 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7408 (tm) REVERT: F 91 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7801 (ttm-80) REVERT: F 92 ASN cc_start: 0.8306 (t0) cc_final: 0.8026 (t0) REVERT: G 81 MET cc_start: 0.8124 (ttp) cc_final: 0.7805 (ttp) REVERT: H 61 MET cc_start: 0.8187 (mmt) cc_final: 0.7879 (mtp) REVERT: H 81 MET cc_start: 0.8406 (ttp) cc_final: 0.8171 (ttp) REVERT: H 102 TYR cc_start: 0.7402 (m-10) cc_final: 0.7200 (m-10) REVERT: I 102 TYR cc_start: 0.7669 (m-10) cc_final: 0.7386 (m-10) outliers start: 46 outliers final: 13 residues processed: 337 average time/residue: 1.1511 time to fit residues: 440.6008 Evaluate side-chains 281 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 267 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 181 LYS Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 288 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 202 optimal weight: 0.0970 chunk 219 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 298 GLN 1 379 GLN 1 428 HIS 1 527 GLN ** 3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 3 269 GLN 9 35 GLN ** 9 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17635 Z= 0.194 Angle : 0.494 7.937 23931 Z= 0.255 Chirality : 0.036 0.136 2829 Planarity : 0.004 0.053 3016 Dihedral : 4.139 28.004 2411 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.54 % Favored : 98.41 % Rotamer: Outliers : 3.37 % Allowed : 14.54 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.18), residues: 2271 helix: 1.44 (0.12), residues: 1738 sheet: None (None), residues: 0 loop : -0.28 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 583 HIS 0.012 0.001 HIS 1 428 PHE 0.015 0.001 PHE 1 529 TYR 0.023 0.002 TYR G 102 ARG 0.009 0.000 ARG I 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 295 time to evaluate : 1.889 Fit side-chains REVERT: 0 34 ARG cc_start: 0.7930 (ptt-90) cc_final: 0.7299 (ptt-90) REVERT: 0 41 GLU cc_start: 0.5177 (OUTLIER) cc_final: 0.4144 (pp20) REVERT: 0 44 ASN cc_start: 0.8684 (m110) cc_final: 0.8397 (m-40) REVERT: 1 194 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7201 (ttmp) REVERT: 1 224 LYS cc_start: 0.8413 (mtmm) cc_final: 0.7439 (pptt) REVERT: 1 387 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7456 (mtm-85) REVERT: 1 415 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7418 (tm-30) REVERT: 1 441 PHE cc_start: 0.8011 (m-80) cc_final: 0.7791 (m-80) REVERT: 1 452 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7393 (tm-30) REVERT: 3 151 ASN cc_start: 0.8141 (t0) cc_final: 0.7890 (t160) REVERT: 5 6 GLU cc_start: 0.8015 (tt0) cc_final: 0.7430 (tt0) REVERT: 6 74 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8243 (mt0) REVERT: 6 86 ILE cc_start: 0.8948 (mt) cc_final: 0.8659 (mm) REVERT: 9 1 MET cc_start: 0.2947 (tmt) cc_final: -0.1265 (mtm) REVERT: 9 9 LYS cc_start: 0.6983 (ttpt) cc_final: 0.6423 (ttpp) REVERT: 9 95 LYS cc_start: 0.7823 (mmtm) cc_final: 0.7566 (mmtp) REVERT: D 119 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7491 (tm) REVERT: F 91 ARG cc_start: 0.8108 (ttm110) cc_final: 0.7833 (ttm-80) REVERT: F 92 ASN cc_start: 0.8437 (t0) cc_final: 0.8125 (t0) REVERT: G 81 MET cc_start: 0.8211 (ttp) cc_final: 0.7861 (ttp) REVERT: H 81 MET cc_start: 0.8357 (ttp) cc_final: 0.8152 (ttp) REVERT: J 111 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7335 (mt-10) REVERT: M 225 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7368 (mm-30) outliers start: 60 outliers final: 23 residues processed: 333 average time/residue: 1.1967 time to fit residues: 449.9068 Evaluate side-chains 309 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 281 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 194 LYS Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 500 LEU Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 235 ASP Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 288 SER Chi-restraints excluded: chain 3 residue 293 SER Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 74 GLN Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain M residue 110 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 200 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 203 optimal weight: 0.7980 chunk 215 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 192 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 379 GLN 1 428 HIS ** 3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 3 269 GLN 9 35 GLN ** 9 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 98 GLN H 98 GLN J 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17635 Z= 0.174 Angle : 0.476 8.295 23931 Z= 0.245 Chirality : 0.036 0.141 2829 Planarity : 0.004 0.054 3016 Dihedral : 4.025 27.988 2411 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 3.31 % Allowed : 15.22 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.18), residues: 2271 helix: 1.78 (0.12), residues: 1737 sheet: None (None), residues: 0 loop : -0.13 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 583 HIS 0.012 0.001 HIS 1 428 PHE 0.026 0.001 PHE G 116 TYR 0.023 0.001 TYR J 102 ARG 0.009 0.000 ARG 1 453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 289 time to evaluate : 1.924 Fit side-chains revert: symmetry clash REVERT: 0 34 ARG cc_start: 0.7957 (ptt-90) cc_final: 0.7290 (ptt-90) REVERT: 0 41 GLU cc_start: 0.4493 (OUTLIER) cc_final: 0.3901 (pm20) REVERT: 0 44 ASN cc_start: 0.8683 (m110) cc_final: 0.8435 (m-40) REVERT: 1 34 GLU cc_start: 0.7895 (pm20) cc_final: 0.7578 (tp30) REVERT: 1 224 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7421 (pptt) REVERT: 1 387 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7429 (mtm-85) REVERT: 1 415 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7347 (tm-30) REVERT: 1 441 PHE cc_start: 0.7942 (m-80) cc_final: 0.7714 (m-80) REVERT: 1 452 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7396 (tm-30) REVERT: 5 6 GLU cc_start: 0.7961 (tt0) cc_final: 0.7371 (tt0) REVERT: 6 86 ILE cc_start: 0.8924 (mt) cc_final: 0.8644 (mm) REVERT: 6 151 LEU cc_start: 0.7821 (pp) cc_final: 0.7585 (pp) REVERT: 9 1 MET cc_start: 0.2939 (tmt) cc_final: -0.1348 (mtm) REVERT: 9 9 LYS cc_start: 0.7060 (ttpt) cc_final: 0.6473 (ttpp) REVERT: 9 35 GLN cc_start: 0.7810 (mt0) cc_final: 0.7487 (mt0) REVERT: A 91 ARG cc_start: 0.7460 (ttm-80) cc_final: 0.7058 (ttp-110) REVERT: D 116 PHE cc_start: 0.7492 (m-10) cc_final: 0.7197 (m-10) REVERT: D 119 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7470 (tm) REVERT: F 91 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7908 (ttm-80) REVERT: F 92 ASN cc_start: 0.8479 (t0) cc_final: 0.8166 (t0) REVERT: G 81 MET cc_start: 0.8179 (ttp) cc_final: 0.7817 (ttp) REVERT: H 61 MET cc_start: 0.8064 (mmt) cc_final: 0.7817 (mtp) REVERT: H 81 MET cc_start: 0.8270 (ttp) cc_final: 0.8047 (ttp) REVERT: I 84 SER cc_start: 0.8969 (m) cc_final: 0.8645 (p) REVERT: J 59 SER cc_start: 0.9044 (m) cc_final: 0.8626 (p) REVERT: J 111 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: M 225 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7431 (mm-30) outliers start: 59 outliers final: 24 residues processed: 323 average time/residue: 1.1348 time to fit residues: 414.9347 Evaluate side-chains 300 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 273 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 500 LEU Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 255 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 179 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 3 optimal weight: 0.0050 chunk 160 optimal weight: 2.9990 chunk 88 optimal weight: 0.0040 chunk 183 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 55 GLN 1 394 GLN 1 428 HIS ** 3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 3 269 GLN ** 9 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN G 98 GLN H 98 GLN I 92 ASN J 98 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17635 Z= 0.190 Angle : 0.482 8.115 23931 Z= 0.247 Chirality : 0.036 0.125 2829 Planarity : 0.004 0.055 3016 Dihedral : 3.988 27.254 2411 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.20 % Allowed : 16.00 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.18), residues: 2271 helix: 1.94 (0.12), residues: 1737 sheet: None (None), residues: 0 loop : -0.09 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 583 HIS 0.011 0.001 HIS 1 428 PHE 0.022 0.001 PHE G 116 TYR 0.020 0.001 TYR A 102 ARG 0.010 0.000 ARG I 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 278 time to evaluate : 1.918 Fit side-chains REVERT: 0 34 ARG cc_start: 0.7963 (ptt-90) cc_final: 0.7313 (ptt-90) REVERT: 0 41 GLU cc_start: 0.4459 (OUTLIER) cc_final: 0.3848 (pm20) REVERT: 0 44 ASN cc_start: 0.8677 (m110) cc_final: 0.8464 (m-40) REVERT: 1 34 GLU cc_start: 0.7889 (pm20) cc_final: 0.7574 (tp30) REVERT: 1 109 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7717 (mmmt) REVERT: 1 195 LYS cc_start: 0.7908 (mmmm) cc_final: 0.7489 (pttm) REVERT: 1 224 LYS cc_start: 0.8427 (mtmm) cc_final: 0.7403 (pptt) REVERT: 1 387 ARG cc_start: 0.7926 (mtp180) cc_final: 0.7470 (mtm-85) REVERT: 1 441 PHE cc_start: 0.7961 (m-80) cc_final: 0.7650 (m-80) REVERT: 1 452 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7384 (tm-30) REVERT: 3 98 VAL cc_start: 0.6144 (OUTLIER) cc_final: 0.5728 (t) REVERT: 5 6 GLU cc_start: 0.7969 (tt0) cc_final: 0.7393 (tt0) REVERT: 6 86 ILE cc_start: 0.8926 (mt) cc_final: 0.8647 (mm) REVERT: 6 151 LEU cc_start: 0.7916 (pp) cc_final: 0.7677 (pp) REVERT: 9 1 MET cc_start: 0.2614 (tmt) cc_final: -0.1677 (mtm) REVERT: 9 9 LYS cc_start: 0.7172 (ttpt) cc_final: 0.6597 (ttpp) REVERT: A 91 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.7143 (ttp-110) REVERT: B 81 MET cc_start: 0.8755 (ttp) cc_final: 0.8332 (ttp) REVERT: D 119 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7494 (tm) REVERT: F 91 ARG cc_start: 0.8140 (ttm110) cc_final: 0.7934 (ttm-80) REVERT: F 92 ASN cc_start: 0.8528 (t0) cc_final: 0.8168 (t0) REVERT: G 81 MET cc_start: 0.8194 (ttp) cc_final: 0.7843 (ttp) REVERT: H 61 MET cc_start: 0.8039 (mmt) cc_final: 0.7748 (mtp) REVERT: H 81 MET cc_start: 0.8260 (ttp) cc_final: 0.8053 (ttp) REVERT: I 84 SER cc_start: 0.8950 (m) cc_final: 0.8611 (p) REVERT: J 66 CYS cc_start: 0.8200 (m) cc_final: 0.7810 (m) REVERT: J 111 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7333 (mt-10) outliers start: 57 outliers final: 30 residues processed: 309 average time/residue: 1.1301 time to fit residues: 395.6347 Evaluate side-chains 304 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 269 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 94 VAL Chi-restraints excluded: chain 1 residue 109 LYS Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 500 LEU Chi-restraints excluded: chain 3 residue 98 VAL Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 235 ASP Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 3 residue 293 SER Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 255 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 0.9980 chunk 194 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 53 optimal weight: 0.0020 chunk 215 optimal weight: 0.5980 chunk 179 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 113 optimal weight: 0.0870 overall best weight: 0.4766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 379 GLN 1 428 HIS ** 3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 189 HIS 3 256 GLN 3 269 GLN 9 35 GLN ** 9 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN H 98 GLN I 92 ASN J 98 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17635 Z= 0.156 Angle : 0.463 8.646 23931 Z= 0.238 Chirality : 0.035 0.121 2829 Planarity : 0.003 0.055 3016 Dihedral : 3.908 27.567 2411 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.86 % Allowed : 16.90 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.18), residues: 2271 helix: 2.14 (0.12), residues: 1737 sheet: None (None), residues: 0 loop : -0.02 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 9 73 HIS 0.011 0.001 HIS 1 428 PHE 0.018 0.001 PHE 9 29 TYR 0.025 0.001 TYR J 102 ARG 0.009 0.000 ARG I 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 289 time to evaluate : 2.219 Fit side-chains revert: symmetry clash REVERT: 0 34 ARG cc_start: 0.7958 (ptt-90) cc_final: 0.7289 (ptt-90) REVERT: 0 41 GLU cc_start: 0.4488 (OUTLIER) cc_final: 0.3885 (pm20) REVERT: 1 34 GLU cc_start: 0.7880 (pm20) cc_final: 0.7587 (tp30) REVERT: 1 101 ASN cc_start: 0.8219 (t0) cc_final: 0.7978 (t0) REVERT: 1 109 LYS cc_start: 0.8141 (tptt) cc_final: 0.7699 (mmmt) REVERT: 1 195 LYS cc_start: 0.7955 (mmmm) cc_final: 0.7525 (pttm) REVERT: 1 224 LYS cc_start: 0.8449 (mtmm) cc_final: 0.7404 (pptt) REVERT: 1 387 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7440 (mtm-85) REVERT: 1 438 GLN cc_start: 0.8324 (tp-100) cc_final: 0.8114 (tp-100) REVERT: 1 441 PHE cc_start: 0.7974 (m-80) cc_final: 0.7556 (m-80) REVERT: 1 452 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7362 (tm-30) REVERT: 3 98 VAL cc_start: 0.6455 (OUTLIER) cc_final: 0.6033 (t) REVERT: 5 6 GLU cc_start: 0.7962 (tt0) cc_final: 0.7380 (tt0) REVERT: 6 74 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: 6 86 ILE cc_start: 0.8918 (mt) cc_final: 0.8649 (mm) REVERT: 9 1 MET cc_start: 0.2395 (tmt) cc_final: -0.1636 (mtm) REVERT: 9 9 LYS cc_start: 0.7165 (ttpt) cc_final: 0.6633 (ttpp) REVERT: A 91 ARG cc_start: 0.7528 (ttm-80) cc_final: 0.7098 (ttp-110) REVERT: B 81 MET cc_start: 0.8745 (ttp) cc_final: 0.8321 (ttp) REVERT: D 119 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7561 (tm) REVERT: F 91 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7940 (ttm-80) REVERT: F 92 ASN cc_start: 0.8514 (t0) cc_final: 0.8156 (t0) REVERT: H 61 MET cc_start: 0.7966 (mmt) cc_final: 0.7716 (mtp) REVERT: I 84 SER cc_start: 0.8932 (m) cc_final: 0.8643 (p) REVERT: J 66 CYS cc_start: 0.8164 (m) cc_final: 0.7798 (m) REVERT: J 111 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7310 (mt-10) outliers start: 51 outliers final: 28 residues processed: 317 average time/residue: 1.1668 time to fit residues: 418.2559 Evaluate side-chains 309 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 276 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 3 residue 98 VAL Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 235 ASP Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 74 GLN Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 71 LYS Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 255 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 428 HIS 1 430 GLN ** 3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 3 269 GLN 9 35 GLN E 98 GLN H 98 GLN I 92 ASN J 92 ASN J 98 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17635 Z= 0.319 Angle : 0.539 9.177 23931 Z= 0.276 Chirality : 0.039 0.137 2829 Planarity : 0.004 0.057 3016 Dihedral : 4.120 25.633 2411 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.37 % Allowed : 17.41 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.18), residues: 2271 helix: 1.97 (0.12), residues: 1734 sheet: None (None), residues: 0 loop : -0.10 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 9 73 HIS 0.011 0.001 HIS 1 428 PHE 0.015 0.002 PHE 3 121 TYR 0.030 0.002 TYR J 102 ARG 0.009 0.001 ARG I 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 274 time to evaluate : 1.802 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.4604 (OUTLIER) cc_final: 0.3933 (pm20) REVERT: 1 34 GLU cc_start: 0.7894 (pm20) cc_final: 0.7561 (tp30) REVERT: 1 109 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7737 (mmmt) REVERT: 1 224 LYS cc_start: 0.8477 (mtmm) cc_final: 0.7442 (pptt) REVERT: 1 387 ARG cc_start: 0.7956 (mtp180) cc_final: 0.7486 (mtm-85) REVERT: 1 438 GLN cc_start: 0.8421 (tp-100) cc_final: 0.8211 (tp-100) REVERT: 1 441 PHE cc_start: 0.8023 (m-80) cc_final: 0.7703 (m-80) REVERT: 1 452 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7363 (tm-30) REVERT: 3 98 VAL cc_start: 0.6265 (OUTLIER) cc_final: 0.5799 (t) REVERT: 3 151 ASN cc_start: 0.8431 (t0) cc_final: 0.8097 (t160) REVERT: 6 86 ILE cc_start: 0.8960 (mt) cc_final: 0.8667 (mm) REVERT: 9 9 LYS cc_start: 0.7147 (ttpt) cc_final: 0.6684 (ttpp) REVERT: A 91 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.7096 (ttp-110) REVERT: E 95 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8154 (pt) REVERT: F 91 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7960 (ttm-80) REVERT: F 92 ASN cc_start: 0.8648 (t0) cc_final: 0.8199 (t0) REVERT: H 61 MET cc_start: 0.8017 (mmt) cc_final: 0.7723 (mtp) REVERT: I 92 ASN cc_start: 0.8632 (t0) cc_final: 0.8261 (t0) REVERT: J 66 CYS cc_start: 0.8220 (m) cc_final: 0.7840 (m) REVERT: J 111 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: M 232 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.6936 (mtp180) outliers start: 60 outliers final: 32 residues processed: 309 average time/residue: 1.1327 time to fit residues: 396.0140 Evaluate side-chains 303 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 265 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 94 VAL Chi-restraints excluded: chain 1 residue 109 LYS Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 3 residue 98 VAL Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 3 residue 293 SER Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 71 LYS Chi-restraints excluded: chain 9 residue 32 SER Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 232 ARG Chi-restraints excluded: chain M residue 255 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 168 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 101 ASN 1 394 GLN 1 428 HIS ** 3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 3 269 GLN 9 35 GLN C 98 GLN E 98 GLN G 92 ASN G 98 GLN H 98 GLN J 98 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17635 Z= 0.196 Angle : 0.492 9.812 23931 Z= 0.251 Chirality : 0.036 0.118 2829 Planarity : 0.004 0.056 3016 Dihedral : 4.005 27.655 2411 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.75 % Allowed : 17.86 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.18), residues: 2271 helix: 2.14 (0.12), residues: 1737 sheet: None (None), residues: 0 loop : -0.05 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 583 HIS 0.011 0.001 HIS 1 428 PHE 0.025 0.001 PHE 9 29 TYR 0.032 0.002 TYR A 102 ARG 0.010 0.000 ARG I 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 275 time to evaluate : 1.933 Fit side-chains REVERT: 0 41 GLU cc_start: 0.4441 (OUTLIER) cc_final: 0.3705 (pm20) REVERT: 1 34 GLU cc_start: 0.7863 (pm20) cc_final: 0.7528 (tp30) REVERT: 1 109 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7713 (mmmt) REVERT: 1 224 LYS cc_start: 0.8461 (mtmm) cc_final: 0.7396 (pptt) REVERT: 1 387 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7455 (mtm-85) REVERT: 1 415 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7390 (tm-30) REVERT: 1 438 GLN cc_start: 0.8349 (tp-100) cc_final: 0.8139 (tp-100) REVERT: 1 441 PHE cc_start: 0.7986 (m-80) cc_final: 0.7645 (m-80) REVERT: 1 452 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7349 (tm-30) REVERT: 3 98 VAL cc_start: 0.6454 (OUTLIER) cc_final: 0.6070 (t) REVERT: 3 151 ASN cc_start: 0.8433 (t0) cc_final: 0.8109 (t160) REVERT: 5 112 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7788 (mtm180) REVERT: 6 86 ILE cc_start: 0.8928 (mt) cc_final: 0.8657 (mm) REVERT: 9 1 MET cc_start: 0.2877 (tmt) cc_final: -0.1570 (ptp) REVERT: 9 9 LYS cc_start: 0.7114 (ttpt) cc_final: 0.6653 (ttpp) REVERT: D 119 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7526 (tm) REVERT: E 95 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8125 (pt) REVERT: F 91 ARG cc_start: 0.8105 (ttm110) cc_final: 0.7658 (ttm-80) REVERT: F 92 ASN cc_start: 0.8586 (t0) cc_final: 0.8332 (t0) REVERT: I 84 SER cc_start: 0.8937 (m) cc_final: 0.8623 (p) REVERT: I 92 ASN cc_start: 0.8532 (t0) cc_final: 0.8192 (t0) REVERT: J 59 SER cc_start: 0.9078 (m) cc_final: 0.8676 (p) REVERT: J 66 CYS cc_start: 0.8138 (m) cc_final: 0.7751 (m) REVERT: J 111 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: M 232 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.6935 (mtp180) outliers start: 49 outliers final: 30 residues processed: 304 average time/residue: 1.1151 time to fit residues: 385.8813 Evaluate side-chains 309 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 271 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 94 VAL Chi-restraints excluded: chain 1 residue 101 ASN Chi-restraints excluded: chain 1 residue 109 LYS Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 3 residue 98 VAL Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 3 residue 293 SER Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 71 LYS Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 232 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 205 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 189 optimal weight: 0.4980 chunk 199 optimal weight: 0.6980 chunk 131 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 257 HIS 1 428 HIS ** 3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 3 269 GLN 9 35 GLN E 98 GLN H 98 GLN J 92 ASN J 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17635 Z= 0.181 Angle : 0.489 10.334 23931 Z= 0.250 Chirality : 0.036 0.119 2829 Planarity : 0.004 0.056 3016 Dihedral : 3.957 27.571 2411 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.58 % Allowed : 18.47 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.18), residues: 2271 helix: 2.22 (0.12), residues: 1737 sheet: None (None), residues: 0 loop : -0.00 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 583 HIS 0.011 0.001 HIS 1 428 PHE 0.015 0.001 PHE 3 115 TYR 0.037 0.002 TYR A 102 ARG 0.010 0.000 ARG I 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 272 time to evaluate : 2.463 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.4425 (OUTLIER) cc_final: 0.3701 (pm20) REVERT: 1 34 GLU cc_start: 0.7859 (pm20) cc_final: 0.7526 (tp30) REVERT: 1 109 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7689 (mmmt) REVERT: 1 224 LYS cc_start: 0.8429 (mtmm) cc_final: 0.7392 (pptt) REVERT: 1 387 ARG cc_start: 0.7898 (mtp180) cc_final: 0.7450 (mtm-85) REVERT: 1 415 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7376 (tm-30) REVERT: 1 438 GLN cc_start: 0.8360 (tp-100) cc_final: 0.8151 (tp-100) REVERT: 1 441 PHE cc_start: 0.7957 (m-80) cc_final: 0.7624 (m-80) REVERT: 1 452 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7341 (tm-30) REVERT: 3 98 VAL cc_start: 0.6589 (OUTLIER) cc_final: 0.6183 (t) REVERT: 3 151 ASN cc_start: 0.8436 (t0) cc_final: 0.8110 (t160) REVERT: 5 112 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7786 (mtm180) REVERT: 6 86 ILE cc_start: 0.8919 (mt) cc_final: 0.8667 (mm) REVERT: 9 1 MET cc_start: 0.2815 (tmt) cc_final: -0.1473 (ptp) REVERT: 9 9 LYS cc_start: 0.7198 (ttpt) cc_final: 0.6597 (ttpp) REVERT: B 81 MET cc_start: 0.8737 (ttp) cc_final: 0.8330 (ttp) REVERT: D 119 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7573 (tm) REVERT: E 95 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8107 (pt) REVERT: F 91 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7661 (ttm-80) REVERT: F 92 ASN cc_start: 0.8595 (t0) cc_final: 0.8346 (t0) REVERT: H 61 MET cc_start: 0.8050 (mmt) cc_final: 0.7557 (mtt) REVERT: I 84 SER cc_start: 0.8932 (m) cc_final: 0.8636 (p) REVERT: I 92 ASN cc_start: 0.8508 (t0) cc_final: 0.8159 (t0) REVERT: J 66 CYS cc_start: 0.8106 (m) cc_final: 0.7743 (m) REVERT: J 111 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: M 232 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.6934 (mtp180) outliers start: 46 outliers final: 32 residues processed: 302 average time/residue: 1.1659 time to fit residues: 399.3204 Evaluate side-chains 306 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 266 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 94 VAL Chi-restraints excluded: chain 1 residue 109 LYS Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 3 residue 98 VAL Chi-restraints excluded: chain 3 residue 126 GLU Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 3 residue 293 SER Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 71 LYS Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 232 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 211 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 222 optimal weight: 0.0770 chunk 204 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 101 ASN 1 428 HIS ** 3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 3 269 GLN 6 57 GLN 9 35 GLN E 98 GLN G 98 GLN H 98 GLN J 92 ASN J 98 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17635 Z= 0.177 Angle : 0.486 10.406 23931 Z= 0.249 Chirality : 0.036 0.119 2829 Planarity : 0.004 0.056 3016 Dihedral : 3.932 27.435 2411 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.53 % Allowed : 18.59 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.18), residues: 2271 helix: 2.28 (0.12), residues: 1736 sheet: None (None), residues: 0 loop : 0.04 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 583 HIS 0.012 0.001 HIS 1 428 PHE 0.022 0.001 PHE F 116 TYR 0.036 0.002 TYR A 102 ARG 0.009 0.000 ARG I 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 276 time to evaluate : 2.047 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.4417 (OUTLIER) cc_final: 0.3586 (pm20) REVERT: 1 34 GLU cc_start: 0.7857 (pm20) cc_final: 0.7526 (tp30) REVERT: 1 109 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7681 (mmmt) REVERT: 1 224 LYS cc_start: 0.8410 (mtmm) cc_final: 0.7369 (pptt) REVERT: 1 387 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7451 (mtm-85) REVERT: 1 415 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7393 (tm-30) REVERT: 1 438 GLN cc_start: 0.8348 (tp-100) cc_final: 0.8138 (tp-100) REVERT: 1 441 PHE cc_start: 0.7962 (m-80) cc_final: 0.7539 (m-80) REVERT: 1 452 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7326 (tm-30) REVERT: 3 98 VAL cc_start: 0.6633 (OUTLIER) cc_final: 0.6232 (t) REVERT: 3 151 ASN cc_start: 0.8439 (t0) cc_final: 0.8113 (t160) REVERT: 5 64 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8260 (tpp-160) REVERT: 5 112 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7784 (mtm180) REVERT: 9 1 MET cc_start: 0.2669 (tmt) cc_final: -0.1529 (ptp) REVERT: 9 9 LYS cc_start: 0.7203 (ttpt) cc_final: 0.6598 (ttpp) REVERT: 9 35 GLN cc_start: 0.7850 (mt0) cc_final: 0.7641 (mt0) REVERT: 9 89 MET cc_start: 0.8133 (mtp) cc_final: 0.7832 (mtp) REVERT: B 81 MET cc_start: 0.8735 (ttp) cc_final: 0.8323 (ttp) REVERT: D 119 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7552 (tm) REVERT: E 95 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8110 (pt) REVERT: F 91 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7661 (ttm-80) REVERT: F 92 ASN cc_start: 0.8601 (t0) cc_final: 0.8370 (t0) REVERT: F 116 PHE cc_start: 0.7441 (m-80) cc_final: 0.7234 (m-80) REVERT: H 61 MET cc_start: 0.8035 (mmt) cc_final: 0.7448 (mtt) REVERT: I 84 SER cc_start: 0.8929 (m) cc_final: 0.8647 (p) REVERT: I 92 ASN cc_start: 0.8445 (t0) cc_final: 0.8101 (t0) REVERT: J 66 CYS cc_start: 0.8024 (m) cc_final: 0.7655 (m) REVERT: J 111 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: M 232 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.6905 (mtp180) outliers start: 45 outliers final: 30 residues processed: 305 average time/residue: 1.1571 time to fit residues: 398.8685 Evaluate side-chains 309 residues out of total 1785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 270 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 94 VAL Chi-restraints excluded: chain 1 residue 101 ASN Chi-restraints excluded: chain 1 residue 109 LYS Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 3 residue 98 VAL Chi-restraints excluded: chain 3 residue 126 GLU Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 3 residue 293 SER Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 71 LYS Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 232 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 0.1980 chunk 54 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 379 GLN 1 428 HIS ** 3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 3 269 GLN 6 57 GLN A 92 ASN E 98 GLN H 98 GLN J 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.096811 restraints weight = 22504.050| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.58 r_work: 0.2940 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17635 Z= 0.210 Angle : 0.711 59.186 23931 Z= 0.414 Chirality : 0.036 0.119 2829 Planarity : 0.004 0.056 3016 Dihedral : 3.963 27.417 2411 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.60 % Favored : 97.36 % Rotamer: Outliers : 2.30 % Allowed : 18.87 % Favored : 78.83 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.18), residues: 2271 helix: 2.28 (0.12), residues: 1736 sheet: None (None), residues: 0 loop : 0.04 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 583 HIS 0.005 0.001 HIS 1 428 PHE 0.023 0.001 PHE F 116 TYR 0.029 0.002 TYR A 102 ARG 0.009 0.000 ARG I 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7259.91 seconds wall clock time: 130 minutes 7.00 seconds (7807.00 seconds total)