Starting phenix.real_space_refine on Fri Feb 16 00:14:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye6_33765/02_2024/7ye6_33765.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye6_33765/02_2024/7ye6_33765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye6_33765/02_2024/7ye6_33765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye6_33765/02_2024/7ye6_33765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye6_33765/02_2024/7ye6_33765.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye6_33765/02_2024/7ye6_33765.pdb" } resolution = 3.4 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= 0.003 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 8707 2.51 5 N 2351 2.21 5 O 2706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 28": "OD1" <-> "OD2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 399": "OD1" <-> "OD2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 464": "OD1" <-> "OD2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A ASP 560": "OD1" <-> "OD2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 685": "OD1" <-> "OD2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 703": "OD1" <-> "OD2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B ASP 311": "OD1" <-> "OD2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B ASP 353": "OD1" <-> "OD2" Residue "B ASP 375": "OD1" <-> "OD2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 93": "OD1" <-> "OD2" Residue "D ARG 94": "NH1" <-> "NH2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 172": "OD1" <-> "OD2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 78": "NH1" <-> "NH2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 1021": "OE1" <-> "OE2" Residue "P ASP 1034": "OD1" <-> "OD2" Residue "P TYR 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 1074": "OD1" <-> "OD2" Residue "P ASP 1077": "OD1" <-> "OD2" Residue "P TYR 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 1120": "OD1" <-> "OD2" Residue "P GLU 1172": "OE1" <-> "OE2" Residue "P PHE 1183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 1209": "OD1" <-> "OD2" Residue "P GLU 1267": "OE1" <-> "OE2" Residue "P ARG 1269": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13804 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6205 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 29, 'TRANS': 755} Chain: "B" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2695 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 353} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'ARG%COO:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 390 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "E" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 671 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "P" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2121 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 275} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 7.42, per 1000 atoms: 0.54 Number of scatterers: 13804 At special positions: 0 Unit cell: (135.876, 120.666, 145.002, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 2706 8.00 N 2351 7.00 C 8707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 427 " - pdb=" SG CYS P1297 " distance=2.04 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " 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: 5.29 Conformation dependent library (CDL) restraints added in 2.5 seconds 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3236 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 18 sheets defined 12.7% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 66 through 71 removed outlier: 4.058A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.602A pdb=" N LEU A 84 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 191 through 197 removed outlier: 4.070A pdb=" N SER A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.631A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 223' Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.574A pdb=" N ARG A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.892A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 303' Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.573A pdb=" N ARG A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 removed outlier: 3.614A pdb=" N ARG A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.805A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.665A pdb=" N LEU B 322 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 319 through 323' Processing helix chain 'D' and resid 32 through 37 removed outlier: 3.993A pdb=" N TYR D 36 " --> pdb=" O PRO D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.434A pdb=" N LEU D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.883A pdb=" N ALA D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 74 through 79' Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.703A pdb=" N ALA D 90 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE D 92 " --> pdb=" O GLN D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 92' Processing helix chain 'D' and resid 93 through 98 removed outlier: 4.434A pdb=" N ARG D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 98' Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.626A pdb=" N MET D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 removed outlier: 4.338A pdb=" N ASP D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 151 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 174 removed outlier: 4.051A pdb=" N LYS D 165 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL D 168 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 189 removed outlier: 3.727A pdb=" N TYR D 179 " --> pdb=" O ALA D 175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.657A pdb=" N VAL D 195 " --> pdb=" O TRP D 191 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 199 " --> pdb=" O VAL D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 215 removed outlier: 4.139A pdb=" N ASP D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 215 " --> pdb=" O THR D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 225 removed outlier: 3.845A pdb=" N GLU D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.580A pdb=" N VAL E 55 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 1012 through 1020 removed outlier: 4.132A pdb=" N LYS P1016 " --> pdb=" O SER P1012 " (cutoff:3.500A) Processing helix chain 'P' and resid 1024 through 1029 removed outlier: 3.682A pdb=" N ARG P1028 " --> pdb=" O ASN P1024 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET P1029 " --> pdb=" O LEU P1025 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 1024 through 1029' Processing sheet with id=AA1, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.241A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 336 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG A 338 " --> pdb=" O MET A 325 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET A 325 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.622A pdb=" N ARG A 353 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 416 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 455 through 457 removed outlier: 3.512A pdb=" N SER A 484 " --> pdb=" O GLY A 516 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 529 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 525 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 565 through 569 removed outlier: 3.836A pdb=" N THR A 617 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP A 745 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 771 " --> pdb=" O PHE A 738 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 777 through 778 Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 51 removed outlier: 4.610A pdb=" N THR B 50 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL B 387 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE B 380 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 390 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 374 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 379 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 67 removed outlier: 4.029A pdb=" N VAL B 81 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL B 95 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 116 through 117 removed outlier: 4.117A pdb=" N THR B 116 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 131 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR B 145 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.655A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 185 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.775A pdb=" N VAL B 252 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 296 through 299 Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 332 removed outlier: 3.804A pdb=" N VAL B 331 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS B 347 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 34 removed outlier: 3.546A pdb=" N GLN E 79 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR E 90 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 65 through 66 removed outlier: 3.991A pdb=" N ASP E 66 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR E 72 " --> pdb=" O ASP E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'P' and resid 1042 through 1043 removed outlier: 4.731A pdb=" N TRP P1042 " --> pdb=" O GLY P1066 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY P1066 " --> pdb=" O TRP P1042 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP P1088 " --> pdb=" O THR P1061 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY P1081 " --> pdb=" O TYR P1108 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS P1101 " --> pdb=" O ASP P1129 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP P1129 " --> pdb=" O LYS P1101 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR P1175 " --> pdb=" O ALA P1151 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY P1204 " --> pdb=" O PHE P1231 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL P1208 " --> pdb=" O LEU P1227 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY P1228 " --> pdb=" O LEU P1259 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG P1257 " --> pdb=" O GLN P1230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 1042 through 1043 removed outlier: 4.731A pdb=" N TRP P1042 " --> pdb=" O GLY P1066 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY P1066 " --> pdb=" O TRP P1042 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR P1049 " --> pdb=" O ASP P1289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 1213 through 1215 removed outlier: 3.586A pdb=" N LYS P1220 " --> pdb=" O GLU P1267 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 846 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: 4.34 Time building geometry restraints manager: 5.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4604 1.34 - 1.46: 3338 1.46 - 1.58: 6086 1.58 - 1.70: 1 1.70 - 1.82: 76 Bond restraints: 14105 Sorted by residual: bond pdb=" C PRO A 721 " pdb=" N THR A 722 " ideal model delta sigma weight residual 1.331 1.369 -0.038 2.07e-02 2.33e+03 3.43e+00 bond pdb=" CA THR B 315 " pdb=" CB THR B 315 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 2.02e+00 bond pdb=" N GLN A 87 " pdb=" CA GLN A 87 " ideal model delta sigma weight residual 1.460 1.479 -0.019 1.45e-02 4.76e+03 1.79e+00 bond pdb=" CB ARG B 273 " pdb=" CG ARG B 273 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" CA LEU A 365 " pdb=" CB LEU A 365 " ideal model delta sigma weight residual 1.539 1.604 -0.064 4.88e-02 4.20e+02 1.73e+00 ... (remaining 14100 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.38: 328 106.38 - 113.40: 7376 113.40 - 120.42: 5253 120.42 - 127.44: 6067 127.44 - 134.46: 136 Bond angle restraints: 19160 Sorted by residual: angle pdb=" CA LEU E 101 " pdb=" CB LEU E 101 " pdb=" CG LEU E 101 " ideal model delta sigma weight residual 116.30 134.46 -18.16 3.50e+00 8.16e-02 2.69e+01 angle pdb=" C VAL B 254 " pdb=" N ASN B 255 " pdb=" CA ASN B 255 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C VAL B 314 " pdb=" N THR B 315 " pdb=" CA THR B 315 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" CA TYR A 504 " pdb=" CB TYR A 504 " pdb=" CG TYR A 504 " ideal model delta sigma weight residual 113.90 121.23 -7.33 1.80e+00 3.09e-01 1.66e+01 angle pdb=" C GLY C 55 " pdb=" N MET C 56 " pdb=" CA MET C 56 " ideal model delta sigma weight residual 121.54 129.19 -7.65 1.91e+00 2.74e-01 1.60e+01 ... (remaining 19155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 7486 17.30 - 34.61: 639 34.61 - 51.91: 123 51.91 - 69.22: 17 69.22 - 86.52: 12 Dihedral angle restraints: 8277 sinusoidal: 3175 harmonic: 5102 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual 93.00 13.70 79.30 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CA CYS P1297 " pdb=" C CYS P1297 " pdb=" N TYR P1298 " pdb=" CA TYR P1298 " ideal model delta harmonic sigma weight residual 180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CB CYS A 427 " pdb=" SG CYS A 427 " pdb=" SG CYS P1297 " pdb=" CB CYS P1297 " ideal model delta sinusoidal sigma weight residual 93.00 41.88 51.12 1 1.00e+01 1.00e-02 3.57e+01 ... (remaining 8274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1740 0.062 - 0.124: 308 0.124 - 0.187: 32 0.187 - 0.249: 4 0.249 - 0.311: 1 Chirality restraints: 2085 Sorted by residual: chirality pdb=" CB VAL D 234 " pdb=" CA VAL D 234 " pdb=" CG1 VAL D 234 " pdb=" CG2 VAL D 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA CYS A 427 " pdb=" N CYS A 427 " pdb=" C CYS A 427 " pdb=" CB CYS A 427 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA CYS P1297 " pdb=" N CYS P1297 " pdb=" C CYS P1297 " pdb=" CB CYS P1297 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2082 not shown) Planarity restraints: 2518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 215 " 0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO D 216 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 216 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 216 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 722 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO A 723 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 723 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 723 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 67 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO C 68 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 68 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 68 " -0.027 5.00e-02 4.00e+02 ... (remaining 2515 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2894 2.78 - 3.31: 11119 3.31 - 3.84: 22503 3.84 - 4.37: 24433 4.37 - 4.90: 43008 Nonbonded interactions: 103957 Sorted by model distance: nonbonded pdb=" OG SER B 285 " pdb=" O VAL B 299 " model vdw 2.254 2.440 nonbonded pdb=" O SER A 761 " pdb=" OG SER A 761 " model vdw 2.323 2.440 nonbonded pdb=" OG SER A 715 " pdb=" OD1 ASP A 740 " model vdw 2.329 2.440 nonbonded pdb=" O SER B 112 " pdb=" OG SER B 112 " model vdw 2.333 2.440 nonbonded pdb=" OG SER A 274 " pdb=" O VAL A 339 " model vdw 2.345 2.440 ... (remaining 103952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 3.760 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 37.570 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14105 Z= 0.190 Angle : 0.677 18.161 19160 Z= 0.365 Chirality : 0.048 0.311 2085 Planarity : 0.004 0.055 2518 Dihedral : 13.340 86.522 5035 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.28 % Allowed : 7.52 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.95 (0.15), residues: 1765 helix: -5.24 (0.09), residues: 184 sheet: -2.71 (0.21), residues: 484 loop : -3.36 (0.14), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 279 HIS 0.002 0.000 HIS A 533 PHE 0.013 0.001 PHE B 104 TYR 0.014 0.001 TYR E 28 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 251 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7921 (pp) REVERT: A 387 GLU cc_start: 0.6840 (pt0) cc_final: 0.6610 (tm-30) REVERT: A 390 ASN cc_start: 0.8125 (t0) cc_final: 0.7795 (p0) REVERT: A 399 ASP cc_start: 0.6410 (m-30) cc_final: 0.5816 (m-30) REVERT: A 519 ILE cc_start: 0.7940 (tp) cc_final: 0.7551 (tp) REVERT: A 601 ILE cc_start: 0.7569 (pt) cc_final: 0.6876 (mm) REVERT: A 736 SER cc_start: 0.8183 (m) cc_final: 0.7843 (t) REVERT: B 306 MET cc_start: 0.3219 (pmm) cc_final: 0.1564 (pmm) REVERT: E 28 TYR cc_start: 0.5201 (p90) cc_final: 0.4630 (t80) REVERT: E 31 ASP cc_start: 0.7053 (p0) cc_final: 0.6581 (p0) REVERT: P 1154 GLU cc_start: 0.6945 (tp30) cc_final: 0.6687 (tp30) REVERT: P 1170 GLN cc_start: 0.6916 (mt0) cc_final: 0.6493 (tt0) outliers start: 4 outliers final: 2 residues processed: 255 average time/residue: 0.3187 time to fit residues: 111.3995 Evaluate side-chains 167 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 268 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 30.0000 chunk 102 optimal weight: 0.0270 chunk 158 optimal weight: 9.9990 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 185 ASN A 265 GLN A 371 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN A 561 GLN A 678 GLN B 40 ASN B 130 GLN B 175 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN D 224 GLN E 34 GLN E 83 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14105 Z= 0.204 Angle : 0.570 14.252 19160 Z= 0.297 Chirality : 0.044 0.172 2085 Planarity : 0.004 0.064 2518 Dihedral : 4.079 46.867 1952 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.42 % Allowed : 15.04 % Favored : 82.54 % 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: -4.28 (0.17), residues: 1765 helix: -4.18 (0.22), residues: 177 sheet: -2.44 (0.21), residues: 490 loop : -2.92 (0.16), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 546 HIS 0.010 0.001 HIS B 121 PHE 0.017 0.001 PHE P1214 TYR 0.032 0.002 TYR A 477 ARG 0.012 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 ASP cc_start: 0.5755 (m-30) cc_final: 0.5108 (m-30) REVERT: A 459 ASN cc_start: 0.7169 (t0) cc_final: 0.6856 (t0) REVERT: A 519 ILE cc_start: 0.8390 (tp) cc_final: 0.7924 (tp) REVERT: A 630 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6872 (mp) REVERT: B 82 LYS cc_start: 0.3823 (mtmm) cc_final: 0.3314 (mtmt) REVERT: B 221 MET cc_start: 0.6961 (ptm) cc_final: 0.6687 (ptp) REVERT: E 28 TYR cc_start: 0.6395 (p90) cc_final: 0.4738 (t80) REVERT: E 31 ASP cc_start: 0.7249 (p0) cc_final: 0.6938 (p0) outliers start: 35 outliers final: 20 residues processed: 193 average time/residue: 0.2940 time to fit residues: 80.7725 Evaluate side-chains 168 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1172 GLU Chi-restraints excluded: chain P residue 1209 ASP Chi-restraints excluded: chain P residue 1262 VAL Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 50.0000 chunk 49 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN A 533 HIS A 538 ASN A 563 ASN A 579 ASN A 625 HIS ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN E 34 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 14105 Z= 0.432 Angle : 0.724 12.796 19160 Z= 0.386 Chirality : 0.046 0.194 2085 Planarity : 0.005 0.085 2518 Dihedral : 4.753 35.540 1949 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 4.28 % Allowed : 19.19 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.91 (0.18), residues: 1765 helix: -3.25 (0.28), residues: 193 sheet: -2.17 (0.23), residues: 484 loop : -2.78 (0.16), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 776 HIS 0.009 0.002 HIS A 677 PHE 0.043 0.002 PHE A 426 TYR 0.037 0.002 TYR A 794 ARG 0.006 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 158 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7421 (m-10) REVERT: A 504 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.8281 (p90) REVERT: A 512 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7698 (p0) REVERT: A 630 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7327 (mp) REVERT: B 82 LYS cc_start: 0.3984 (mtmm) cc_final: 0.3310 (mtmt) REVERT: B 221 MET cc_start: 0.6981 (ptm) cc_final: 0.6744 (ptp) REVERT: D 204 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.6372 (p0) REVERT: P 1018 PHE cc_start: 0.8080 (t80) cc_final: 0.7786 (t80) REVERT: P 1058 ASP cc_start: 0.7386 (m-30) cc_final: 0.7013 (m-30) outliers start: 62 outliers final: 43 residues processed: 203 average time/residue: 0.2779 time to fit residues: 81.9488 Evaluate side-chains 189 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1100 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1121 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1172 GLU Chi-restraints excluded: chain P residue 1209 ASP Chi-restraints excluded: chain P residue 1221 VAL Chi-restraints excluded: chain P residue 1262 VAL Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 82 optimal weight: 0.2980 chunk 17 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 106 optimal weight: 50.0000 chunk 159 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN B 64 HIS ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14105 Z= 0.211 Angle : 0.575 13.415 19160 Z= 0.302 Chirality : 0.044 0.252 2085 Planarity : 0.004 0.060 2518 Dihedral : 4.277 30.291 1949 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.73 % Allowed : 21.12 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.58 (0.18), residues: 1765 helix: -2.82 (0.31), residues: 191 sheet: -1.97 (0.22), residues: 491 loop : -2.59 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 546 HIS 0.006 0.001 HIS A 677 PHE 0.016 0.001 PHE A 426 TYR 0.023 0.001 TYR A 794 ARG 0.005 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 154 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7996 (pp) REVERT: A 428 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7407 (m-10) REVERT: B 82 LYS cc_start: 0.4068 (mtmm) cc_final: 0.3702 (mtmt) REVERT: B 221 MET cc_start: 0.6981 (ptm) cc_final: 0.6743 (ptp) REVERT: D 174 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7884 (pp) REVERT: E 28 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.5006 (t80) REVERT: E 31 ASP cc_start: 0.7167 (p0) cc_final: 0.6931 (p0) REVERT: P 1018 PHE cc_start: 0.8194 (t80) cc_final: 0.7905 (t80) outliers start: 54 outliers final: 33 residues processed: 193 average time/residue: 0.2751 time to fit residues: 77.0747 Evaluate side-chains 177 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1209 ASP Chi-restraints excluded: chain P residue 1262 VAL Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 1.9990 chunk 96 optimal weight: 30.0000 chunk 2 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 42 optimal weight: 0.0970 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN B 70 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS C 34 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14105 Z= 0.191 Angle : 0.568 13.901 19160 Z= 0.295 Chirality : 0.043 0.247 2085 Planarity : 0.004 0.040 2518 Dihedral : 4.144 29.782 1949 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.28 % Allowed : 21.95 % Favored : 73.78 % 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: -3.52 (0.18), residues: 1765 helix: -2.46 (0.32), residues: 211 sheet: -1.89 (0.22), residues: 505 loop : -2.62 (0.17), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 546 HIS 0.011 0.001 HIS B 324 PHE 0.017 0.001 PHE A 426 TYR 0.017 0.001 TYR A 794 ARG 0.005 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 154 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7918 (pp) REVERT: A 428 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7260 (m-10) REVERT: A 791 PHE cc_start: 0.6252 (t80) cc_final: 0.5742 (t80) REVERT: B 82 LYS cc_start: 0.4035 (mtmm) cc_final: 0.3468 (mtmt) REVERT: B 221 MET cc_start: 0.6969 (ptm) cc_final: 0.6736 (ptp) REVERT: D 174 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7899 (pp) REVERT: D 233 LYS cc_start: 0.4763 (OUTLIER) cc_final: 0.4522 (pttm) REVERT: E 28 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.4510 (t80) REVERT: E 31 ASP cc_start: 0.7276 (p0) cc_final: 0.7012 (p0) REVERT: P 1018 PHE cc_start: 0.8189 (t80) cc_final: 0.7943 (t80) REVERT: P 1227 LEU cc_start: 0.8763 (tp) cc_final: 0.8440 (mp) outliers start: 62 outliers final: 42 residues processed: 199 average time/residue: 0.2640 time to fit residues: 76.2818 Evaluate side-chains 193 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 146 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain P residue 1063 VAL Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1146 THR Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1209 ASP Chi-restraints excluded: chain P residue 1262 VAL Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 50.0000 chunk 41 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 14105 Z= 0.393 Angle : 0.704 14.169 19160 Z= 0.374 Chirality : 0.047 0.253 2085 Planarity : 0.005 0.090 2518 Dihedral : 4.814 34.898 1949 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 5.45 % Allowed : 21.81 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.44 (0.18), residues: 1765 helix: -2.24 (0.33), residues: 207 sheet: -1.93 (0.23), residues: 493 loop : -2.56 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 745 HIS 0.008 0.002 HIS A 677 PHE 0.034 0.002 PHE A 426 TYR 0.030 0.002 TYR A 794 ARG 0.004 0.001 ARG A 592 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 152 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7110 (pp) REVERT: A 365 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8120 (pp) REVERT: A 428 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7362 (m-10) REVERT: A 504 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8264 (p90) REVERT: B 82 LYS cc_start: 0.3973 (mtmm) cc_final: 0.3664 (mtmt) REVERT: B 221 MET cc_start: 0.6971 (ptm) cc_final: 0.6758 (ptp) REVERT: D 174 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7933 (pp) REVERT: E 28 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.3944 (t80) REVERT: E 31 ASP cc_start: 0.7387 (p0) cc_final: 0.7168 (p0) REVERT: P 1205 ARG cc_start: 0.8278 (tmm-80) cc_final: 0.8048 (ttp80) outliers start: 79 outliers final: 58 residues processed: 209 average time/residue: 0.2816 time to fit residues: 85.4152 Evaluate side-chains 206 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 142 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain P residue 1063 VAL Chi-restraints excluded: chain P residue 1080 THR Chi-restraints excluded: chain P residue 1084 VAL Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1146 THR Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1172 GLU Chi-restraints excluded: chain P residue 1203 ILE Chi-restraints excluded: chain P residue 1209 ASP Chi-restraints excluded: chain P residue 1221 VAL Chi-restraints excluded: chain P residue 1261 SER Chi-restraints excluded: chain P residue 1262 VAL Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.0040 chunk 96 optimal weight: 40.0000 chunk 123 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 94 optimal weight: 50.0000 chunk 168 optimal weight: 0.4980 chunk 105 optimal weight: 20.0000 chunk 102 optimal weight: 50.0000 chunk 77 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 overall best weight: 5.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS D 60 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.156 14105 Z= 0.555 Angle : 0.839 17.155 19160 Z= 0.449 Chirality : 0.051 0.325 2085 Planarity : 0.006 0.090 2518 Dihedral : 5.531 39.443 1949 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Rotamer: Outliers : 5.73 % Allowed : 23.19 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.60 (0.18), residues: 1765 helix: -2.26 (0.32), residues: 212 sheet: -2.05 (0.23), residues: 468 loop : -2.69 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 206 HIS 0.011 0.002 HIS P1128 PHE 0.036 0.003 PHE A 426 TYR 0.038 0.003 TYR A 794 ARG 0.006 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 143 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.2204 (OUTLIER) cc_final: 0.1777 (m) REVERT: A 365 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8240 (pp) REVERT: A 428 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: A 504 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8399 (p90) REVERT: A 791 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.5516 (t80) REVERT: B 82 LYS cc_start: 0.4088 (mtmm) cc_final: 0.3882 (mtmt) REVERT: D 174 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8019 (pp) REVERT: D 204 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.6322 (p0) REVERT: P 1231 PHE cc_start: 0.6063 (t80) cc_final: 0.5840 (t80) outliers start: 83 outliers final: 63 residues processed: 207 average time/residue: 0.2405 time to fit residues: 73.9274 Evaluate side-chains 207 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 137 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain P residue 1063 VAL Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1088 ASP Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1146 THR Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1172 GLU Chi-restraints excluded: chain P residue 1206 THR Chi-restraints excluded: chain P residue 1209 ASP Chi-restraints excluded: chain P residue 1218 ASP Chi-restraints excluded: chain P residue 1221 VAL Chi-restraints excluded: chain P residue 1261 SER Chi-restraints excluded: chain P residue 1262 VAL Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1296 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 8.9990 chunk 100 optimal weight: 50.0000 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 114 optimal weight: 0.1980 chunk 83 optimal weight: 6.9990 chunk 15 optimal weight: 40.0000 chunk 132 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS D 60 ASN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 14105 Z= 0.358 Angle : 0.716 14.541 19160 Z= 0.377 Chirality : 0.047 0.319 2085 Planarity : 0.005 0.071 2518 Dihedral : 5.104 36.119 1949 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 5.24 % Allowed : 24.09 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.45 (0.18), residues: 1765 helix: -2.07 (0.33), residues: 212 sheet: -1.97 (0.24), residues: 460 loop : -2.59 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 206 HIS 0.006 0.001 HIS A 677 PHE 0.025 0.002 PHE A 494 TYR 0.040 0.002 TYR P1144 ARG 0.005 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 147 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.1875 (OUTLIER) cc_final: 0.1558 (m) REVERT: A 365 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8109 (pp) REVERT: A 428 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: A 504 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8318 (p90) REVERT: A 791 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.5425 (t80) REVERT: B 82 LYS cc_start: 0.4012 (mtmm) cc_final: 0.3596 (mtmt) REVERT: D 174 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7946 (pp) outliers start: 76 outliers final: 62 residues processed: 208 average time/residue: 0.2478 time to fit residues: 76.3332 Evaluate side-chains 212 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 144 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain P residue 1063 VAL Chi-restraints excluded: chain P residue 1084 VAL Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1088 ASP Chi-restraints excluded: chain P residue 1100 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1121 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1146 THR Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1209 ASP Chi-restraints excluded: chain P residue 1218 ASP Chi-restraints excluded: chain P residue 1221 VAL Chi-restraints excluded: chain P residue 1261 SER Chi-restraints excluded: chain P residue 1262 VAL Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1296 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 8.9990 chunk 147 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 94 optimal weight: 30.0000 chunk 68 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** P1128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14105 Z= 0.269 Angle : 0.675 14.592 19160 Z= 0.350 Chirality : 0.046 0.300 2085 Planarity : 0.004 0.060 2518 Dihedral : 4.853 33.920 1949 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 4.97 % Allowed : 24.36 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.27 (0.19), residues: 1765 helix: -1.85 (0.34), residues: 212 sheet: -1.84 (0.24), residues: 459 loop : -2.49 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 546 HIS 0.005 0.001 HIS A 677 PHE 0.020 0.002 PHE A 494 TYR 0.032 0.002 TYR P1144 ARG 0.006 0.001 ARG P1142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 153 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.2058 (OUTLIER) cc_final: 0.1734 (m) REVERT: A 109 MET cc_start: 0.4123 (ppp) cc_final: 0.3257 (ppp) REVERT: A 365 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8022 (pp) REVERT: A 428 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: A 504 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8300 (p90) REVERT: A 791 PHE cc_start: 0.6542 (OUTLIER) cc_final: 0.5556 (t80) REVERT: B 82 LYS cc_start: 0.3852 (mtmm) cc_final: 0.3464 (mtmt) REVERT: D 174 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7944 (pp) REVERT: E 28 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.4386 (t80) REVERT: P 1231 PHE cc_start: 0.5739 (t80) cc_final: 0.5520 (t80) outliers start: 72 outliers final: 55 residues processed: 210 average time/residue: 0.2583 time to fit residues: 80.3410 Evaluate side-chains 205 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 143 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain P residue 1006 ASN Chi-restraints excluded: chain P residue 1063 VAL Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1088 ASP Chi-restraints excluded: chain P residue 1095 VAL Chi-restraints excluded: chain P residue 1100 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1146 THR Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1209 ASP Chi-restraints excluded: chain P residue 1218 ASP Chi-restraints excluded: chain P residue 1221 VAL Chi-restraints excluded: chain P residue 1261 SER Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1296 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 115 optimal weight: 0.0270 chunk 174 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 14 optimal weight: 0.0040 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.1454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN D 89 GLN E 52 GLN P1128 HIS P1295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14105 Z= 0.186 Angle : 0.644 14.725 19160 Z= 0.328 Chirality : 0.045 0.272 2085 Planarity : 0.004 0.052 2518 Dihedral : 4.552 29.967 1949 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 4.21 % Allowed : 25.05 % Favored : 70.74 % 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: -3.08 (0.19), residues: 1765 helix: -1.60 (0.35), residues: 199 sheet: -1.78 (0.24), residues: 468 loop : -2.34 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 546 HIS 0.004 0.001 HIS A 677 PHE 0.012 0.001 PHE A 494 TYR 0.030 0.001 TYR P1144 ARG 0.003 0.000 ARG P1273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 155 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.2136 (OUTLIER) cc_final: 0.1758 (m) REVERT: A 109 MET cc_start: 0.3636 (ppp) cc_final: 0.2788 (ppp) REVERT: A 365 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7843 (pp) REVERT: A 428 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: A 504 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.8144 (p90) REVERT: A 791 PHE cc_start: 0.6446 (OUTLIER) cc_final: 0.5490 (t80) REVERT: B 82 LYS cc_start: 0.3591 (mtmm) cc_final: 0.3358 (mtmt) REVERT: B 96 SER cc_start: 0.4578 (t) cc_final: 0.4077 (p) REVERT: D 174 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7893 (pp) REVERT: P 1018 PHE cc_start: 0.8224 (t80) cc_final: 0.7906 (t80) REVERT: P 1227 LEU cc_start: 0.8714 (tp) cc_final: 0.8406 (mp) REVERT: P 1231 PHE cc_start: 0.5735 (t80) cc_final: 0.5522 (t80) outliers start: 61 outliers final: 49 residues processed: 201 average time/residue: 0.2699 time to fit residues: 78.8903 Evaluate side-chains 198 residues out of total 1474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 143 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain P residue 1006 ASN Chi-restraints excluded: chain P residue 1063 VAL Chi-restraints excluded: chain P residue 1085 THR Chi-restraints excluded: chain P residue 1088 ASP Chi-restraints excluded: chain P residue 1100 THR Chi-restraints excluded: chain P residue 1107 LEU Chi-restraints excluded: chain P residue 1121 LEU Chi-restraints excluded: chain P residue 1122 ILE Chi-restraints excluded: chain P residue 1128 HIS Chi-restraints excluded: chain P residue 1146 THR Chi-restraints excluded: chain P residue 1166 TRP Chi-restraints excluded: chain P residue 1209 ASP Chi-restraints excluded: chain P residue 1218 ASP Chi-restraints excluded: chain P residue 1261 SER Chi-restraints excluded: chain P residue 1283 PHE Chi-restraints excluded: chain P residue 1296 PHE Chi-restraints excluded: chain P residue 1297 CYS Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 7.9990 chunk 42 optimal weight: 0.1980 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5099 r_free = 0.5099 target = 0.282316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.226158 restraints weight = 17173.430| |-----------------------------------------------------------------------------| r_work (start): 0.4803 rms_B_bonded: 3.42 r_work: 0.4398 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14105 Z= 0.220 Angle : 0.655 14.756 19160 Z= 0.335 Chirality : 0.045 0.279 2085 Planarity : 0.004 0.048 2518 Dihedral : 4.563 31.492 1949 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 4.21 % Allowed : 25.05 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.07 (0.19), residues: 1765 helix: -1.59 (0.35), residues: 200 sheet: -1.78 (0.24), residues: 473 loop : -2.34 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 546 HIS 0.009 0.001 HIS P1128 PHE 0.016 0.001 PHE A 802 TYR 0.030 0.002 TYR P1144 ARG 0.007 0.001 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2947.10 seconds wall clock time: 54 minutes 19.49 seconds (3259.49 seconds total)