Starting phenix.real_space_refine on Fri Feb 16 00:59:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye4_33763/02_2024/7ye4_33763.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye4_33763/02_2024/7ye4_33763.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/7ye4_33763/02_2024/7ye4_33763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye4_33763/02_2024/7ye4_33763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye4_33763/02_2024/7ye4_33763.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ye4_33763/02_2024/7ye4_33763.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= 0.004 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 42 5.16 5 C 8749 2.51 5 N 2363 2.21 5 O 2723 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 GLU 32": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A ARG 127": "NH1" <-> "NH2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A ASP 622": "OD1" <-> "OD2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A ASP 624": "OD1" <-> "OD2" Residue "A ASP 639": "OD1" <-> "OD2" Residue "A GLU 645": "OE1" <-> "OE2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A ASP 759": "OD1" <-> "OD2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D ASP 84": "OD1" <-> "OD2" Residue "D ARG 94": "NH1" <-> "NH2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "E ARG 78": "NH1" <-> "NH2" Residue "P PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 1077": "OD1" <-> "OD2" Residue "P PHE 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 1129": "OD1" <-> "OD2" Residue "P TYR 1150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 1168": "OE1" <-> "OE2" Residue "P GLU 1172": "OE1" <-> "OE2" Residue "P GLU 1238": "OE1" <-> "OE2" Residue "P GLU 1267": "OE1" <-> "OE2" Residue "P ARG 1269": "NH1" <-> "NH2" Residue "P GLU 1277": "OE1" <-> "OE2" Residue "P ARG 1297": "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: 13877 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6211 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 29, 'TRANS': 755} Chain: "B" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2713 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 355} 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: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 377 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 7, 'TRANS': 46} 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: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "P" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2142 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 278} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 7.00, per 1000 atoms: 0.50 Number of scatterers: 13877 At special positions: 0 Unit cell: (125.736, 133.848, 140.946, 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 42 16.00 O 2723 8.00 N 2363 7.00 C 8749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS P1293 " distance=2.04 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 781 " - pdb=" SG CYS P1043 " 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: 4.75 Conformation dependent library (CDL) restraints added in 2.6 seconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 23 sheets defined 16.8% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.658A pdb=" N THR A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 117 removed outlier: 4.607A pdb=" N ASN A 113 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.614A pdb=" N VAL A 144 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 removed outlier: 4.026A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 195' Processing helix chain 'A' and resid 215 through 230 removed outlier: 3.994A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 removed outlier: 3.584A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 308 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.859A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 391 Processing helix chain 'A' and resid 542 through 552 removed outlier: 4.573A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.935A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 323 removed outlier: 4.035A pdb=" N LEU B 322 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 4.162A 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: 3.604A pdb=" N TYR D 36 " --> pdb=" O PRO D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 54 removed outlier: 4.212A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 49 through 54' Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.615A pdb=" N LEU D 58 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 79 removed outlier: 3.890A pdb=" N ILE D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.677A pdb=" N ALA D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA D 90 " --> pdb=" O PRO D 86 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP D 93 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 removed outlier: 3.519A pdb=" N MET D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY D 113 " --> pdb=" O MET D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 129 removed outlier: 3.587A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 143 Processing helix chain 'D' and resid 144 through 154 removed outlier: 3.843A pdb=" N LYS D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.540A pdb=" N VAL D 168 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 205 removed outlier: 3.578A pdb=" N ARG D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 199 " --> pdb=" O VAL D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 225 removed outlier: 4.076A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.531A pdb=" N TYR D 222 " --> pdb=" O MET D 218 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 239 removed outlier: 3.620A pdb=" N GLU D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 234 " --> pdb=" O GLN D 230 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 237 " --> pdb=" O LYS D 233 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.558A pdb=" N VAL E 55 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 1003 through 1012 removed outlier: 3.944A pdb=" N ALA P1009 " --> pdb=" O ARG P1005 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU P1010 " --> pdb=" O ASN P1006 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE P1011 " --> pdb=" O ALA P1007 " (cutoff:3.500A) Processing helix chain 'P' and resid 1013 through 1022 removed outlier: 3.878A pdb=" N LEU P1019 " --> pdb=" O TYR P1015 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL P1022 " --> pdb=" O PHE P1018 " (cutoff:3.500A) Processing helix chain 'P' and resid 1135 through 1139 removed outlier: 4.276A pdb=" N GLY P1138 " --> pdb=" O THR P1135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 99 removed outlier: 7.779A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 166 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 154 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 168 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS A 152 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 183 removed outlier: 4.453A pdb=" N ILE A 177 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL A 256 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN A 179 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N VAL A 258 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN A 181 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE A 260 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 183 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.856A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 337 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 336 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.574A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 426 through 427 Processing sheet with id=AA6, first strand: chain 'A' and resid 440 through 446 removed outlier: 3.536A pdb=" N THR A 514 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 440 through 446 removed outlier: 3.536A pdb=" N THR A 514 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 785 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.563A pdb=" N VAL B 81 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.769A pdb=" N HIS B 121 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 131 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 145 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.782A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 185 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AB4, first strand: chain 'B' and resid 257 through 258 Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 291 removed outlier: 3.968A pdb=" N ILE B 290 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 297 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AB7, first strand: chain 'B' and resid 372 through 374 removed outlier: 3.692A pdb=" N ILE B 380 " --> pdb=" O TYR B 388 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.085A pdb=" N THR E 72 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AC1, first strand: chain 'P' and resid 1044 through 1047 removed outlier: 3.975A pdb=" N ARG P1044 " --> pdb=" O GLN P1064 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN P1064 " --> pdb=" O ARG P1044 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 1057 through 1058 Processing sheet with id=AC3, first strand: chain 'P' and resid 1081 through 1089 removed outlier: 4.087A pdb=" N GLY P1081 " --> pdb=" O TYR P1108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR P1108 " --> pdb=" O GLY P1081 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR P1132 " --> pdb=" O ARG P1142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 1081 through 1089 removed outlier: 4.087A pdb=" N GLY P1081 " --> pdb=" O TYR P1108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR P1108 " --> pdb=" O GLY P1081 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS P1124 " --> pdb=" O TYR P1150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR P1146 " --> pdb=" O HIS P1128 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG P1205 " --> pdb=" O GLU P1172 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR P1206 " --> pdb=" O TYR P1229 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY P1228 " --> pdb=" O LEU P1259 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG P1257 " --> pdb=" O GLN P1230 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET P1260 " --> pdb=" O LYS P1280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 1165 through 1167 removed outlier: 3.695A pdb=" N VAL P1221 " --> pdb=" O PHE P1214 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS P1220 " --> pdb=" O GLU P1267 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA P1266 " --> pdb=" O ARG P1273 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG P1273 " --> pdb=" O ALA P1266 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1119 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: 4.92 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4632 1.35 - 1.46: 3431 1.46 - 1.58: 6038 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 14179 Sorted by residual: bond pdb=" C VAL A 155 " pdb=" N THR A 156 " ideal model delta sigma weight residual 1.331 1.387 -0.056 2.83e-02 1.25e+03 3.91e+00 bond pdb=" N THR B 315 " pdb=" CA THR B 315 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 2.94e+00 bond pdb=" N ASP A 562 " pdb=" CA ASP A 562 " ideal model delta sigma weight residual 1.460 1.483 -0.023 1.42e-02 4.96e+03 2.62e+00 bond pdb=" CA ASP A 562 " pdb=" CB ASP A 562 " ideal model delta sigma weight residual 1.527 1.551 -0.024 1.61e-02 3.86e+03 2.29e+00 bond pdb=" CA THR B 315 " pdb=" CB THR B 315 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.69e-02 3.50e+03 2.28e+00 ... (remaining 14174 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.09: 374 107.09 - 113.83: 7567 113.83 - 120.57: 5443 120.57 - 127.31: 5747 127.31 - 134.04: 133 Bond angle restraints: 19264 Sorted by residual: angle pdb=" N VAL D 192 " pdb=" CA VAL D 192 " pdb=" C VAL D 192 " ideal model delta sigma weight residual 112.96 107.40 5.56 1.00e+00 1.00e+00 3.09e+01 angle pdb=" C GLN A 561 " pdb=" N ASP A 562 " pdb=" CA ASP A 562 " ideal model delta sigma weight residual 122.82 130.48 -7.66 1.42e+00 4.96e-01 2.91e+01 angle pdb=" C ALA B 374 " pdb=" N ASP B 375 " pdb=" CA ASP B 375 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C LYS A 728 " pdb=" N TYR A 729 " pdb=" CA TYR A 729 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 angle pdb=" C ASN A 161 " pdb=" N ARG A 162 " pdb=" CA ARG A 162 " ideal model delta sigma weight residual 122.82 129.13 -6.31 1.42e+00 4.96e-01 1.98e+01 ... (remaining 19259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7560 17.94 - 35.87: 641 35.87 - 53.81: 105 53.81 - 71.74: 14 71.74 - 89.68: 14 Dihedral angle restraints: 8334 sinusoidal: 3199 harmonic: 5135 Sorted by residual: dihedral pdb=" CA TYR A 729 " pdb=" C TYR A 729 " pdb=" N ALA A 730 " pdb=" CA ALA A 730 " ideal model delta harmonic sigma weight residual 180.00 148.63 31.37 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CB CYS A 431 " pdb=" SG CYS A 431 " pdb=" SG CYS P1293 " pdb=" CB CYS P1293 " ideal model delta sinusoidal sigma weight residual -86.00 -37.14 -48.86 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CA GLU B 282 " pdb=" C GLU B 282 " pdb=" N LEU B 283 " pdb=" CA LEU B 283 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 8331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1617 0.049 - 0.097: 364 0.097 - 0.146: 101 0.146 - 0.194: 10 0.194 - 0.242: 8 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CA ASP A 562 " pdb=" N ASP A 562 " pdb=" C ASP A 562 " pdb=" CB ASP A 562 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA THR B 315 " pdb=" N THR B 315 " pdb=" C THR B 315 " pdb=" CB THR B 315 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR B 315 " pdb=" CA THR B 315 " pdb=" OG1 THR B 315 " pdb=" CG2 THR B 315 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2097 not shown) Planarity restraints: 2533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 370 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO B 371 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 158 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 159 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 720 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A 721 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 721 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 721 " -0.032 5.00e-02 4.00e+02 ... (remaining 2530 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4757 2.86 - 3.37: 11217 3.37 - 3.88: 21840 3.88 - 4.39: 23743 4.39 - 4.90: 42244 Nonbonded interactions: 103801 Sorted by model distance: nonbonded pdb=" OH TYR A 608 " pdb=" OE1 GLU A 650 " model vdw 2.352 2.440 nonbonded pdb=" O SER P1012 " pdb=" OG SER P1012 " model vdw 2.356 2.440 nonbonded pdb=" OE2 GLU A 305 " pdb=" OG SER A 324 " model vdw 2.356 2.440 nonbonded pdb=" OG SER P1092 " pdb=" O PHE P1096 " model vdw 2.357 2.440 nonbonded pdb=" OH TYR D 110 " pdb=" OD2 ASP D 162 " model vdw 2.360 2.440 ... (remaining 103796 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: 0.740 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: 3.610 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 37.370 Find NCS groups from input model: 0.370 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 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 0.056 14179 Z= 0.181 Angle : 0.677 11.444 19264 Z= 0.371 Chirality : 0.047 0.242 2100 Planarity : 0.004 0.063 2533 Dihedral : 13.680 89.677 5065 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.07 % Allowed : 7.68 % Favored : 92.25 % 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: -5.13 (0.15), residues: 1775 helix: -5.11 (0.06), residues: 269 sheet: -2.49 (0.20), residues: 532 loop : -3.51 (0.15), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 776 HIS 0.002 0.000 HIS A 533 PHE 0.023 0.001 PHE A 440 TYR 0.016 0.001 TYR A 686 ARG 0.001 0.000 ARG A 767 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 280 time to evaluate : 1.417 Fit side-chains REVERT: A 646 MET cc_start: 0.6353 (tpt) cc_final: 0.5578 (tpt) REVERT: B 146 LYS cc_start: 0.8146 (tptp) cc_final: 0.7906 (tptp) REVERT: B 192 LEU cc_start: 0.7650 (tp) cc_final: 0.7386 (tt) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.2967 time to fit residues: 116.6792 Evaluate side-chains 190 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.9990 chunk 134 optimal weight: 0.0870 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 90 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN A 244 GLN A 523 ASN A 534 ASN A 677 HIS A 775 GLN A 789 GLN B 175 ASN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN C 71 ASN D 40 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN D 138 GLN D 224 GLN D 228 ASN P1170 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14179 Z= 0.178 Angle : 0.510 8.099 19264 Z= 0.268 Chirality : 0.042 0.172 2100 Planarity : 0.004 0.048 2533 Dihedral : 3.885 28.788 1958 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.78 % Allowed : 14.54 % Favored : 83.68 % 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: -4.20 (0.17), residues: 1775 helix: -3.53 (0.19), residues: 277 sheet: -1.93 (0.22), residues: 512 loop : -3.13 (0.16), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 776 HIS 0.007 0.001 HIS E 83 PHE 0.020 0.001 PHE P1214 TYR 0.017 0.001 TYR A 296 ARG 0.005 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 1.516 Fit side-chains REVERT: A 646 MET cc_start: 0.6926 (tpt) cc_final: 0.5982 (tpt) REVERT: P 1129 ASP cc_start: 0.7117 (m-30) cc_final: 0.6900 (m-30) REVERT: P 1154 GLU cc_start: 0.5100 (tm-30) cc_final: 0.4710 (tm-30) outliers start: 26 outliers final: 21 residues processed: 220 average time/residue: 0.2497 time to fit residues: 81.3149 Evaluate side-chains 200 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 179 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1130 ASN Chi-restraints excluded: chain P residue 1288 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 113 ASN A 748 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN P1026 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14179 Z= 0.295 Angle : 0.586 8.642 19264 Z= 0.308 Chirality : 0.044 0.179 2100 Planarity : 0.004 0.051 2533 Dihedral : 4.434 32.223 1958 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.25 % Allowed : 16.67 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.71 (0.18), residues: 1775 helix: -2.45 (0.24), residues: 300 sheet: -1.78 (0.21), residues: 541 loop : -2.93 (0.18), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 317 HIS 0.006 0.001 HIS E 83 PHE 0.025 0.002 PHE A 791 TYR 0.016 0.002 TYR A 686 ARG 0.005 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 194 time to evaluate : 1.552 Fit side-chains REVERT: A 646 MET cc_start: 0.7924 (tpt) cc_final: 0.7374 (tpt) REVERT: B 146 LYS cc_start: 0.8221 (tptp) cc_final: 0.7919 (tptp) REVERT: P 1072 GLU cc_start: 0.4446 (mm-30) cc_final: 0.1741 (tp30) outliers start: 62 outliers final: 46 residues processed: 241 average time/residue: 0.2535 time to fit residues: 93.5164 Evaluate side-chains 218 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain P residue 1019 LEU Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1129 ASP Chi-restraints excluded: chain P residue 1130 ASN Chi-restraints excluded: chain P residue 1232 ASP Chi-restraints excluded: chain P residue 1288 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 259 ASN A 422 ASN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 60 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN E 79 GLN E 103 ASN P1160 HIS P1295 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 14179 Z= 0.537 Angle : 0.775 10.431 19264 Z= 0.409 Chirality : 0.050 0.190 2100 Planarity : 0.006 0.059 2533 Dihedral : 5.678 37.576 1958 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 5.69 % Allowed : 19.82 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.81 (0.18), residues: 1775 helix: -2.23 (0.26), residues: 311 sheet: -2.12 (0.20), residues: 569 loop : -2.92 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 739 HIS 0.007 0.002 HIS P1062 PHE 0.064 0.003 PHE A 428 TYR 0.029 0.003 TYR B 345 ARG 0.013 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 177 time to evaluate : 1.490 Fit side-chains REVERT: A 545 MET cc_start: 0.7885 (ttm) cc_final: 0.7574 (ttm) REVERT: A 785 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7889 (p90) REVERT: B 191 SER cc_start: 0.8284 (t) cc_final: 0.7802 (p) REVERT: P 1072 GLU cc_start: 0.5478 (mm-30) cc_final: 0.3231 (tp30) REVERT: P 1073 LEU cc_start: 0.1438 (OUTLIER) cc_final: 0.1209 (pt) REVERT: P 1286 TYR cc_start: 0.4511 (m-80) cc_final: 0.4273 (m-10) outliers start: 83 outliers final: 60 residues processed: 241 average time/residue: 0.2320 time to fit residues: 84.1250 Evaluate side-chains 214 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 152 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain P residue 1019 LEU Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1073 LEU Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1129 ASP Chi-restraints excluded: chain P residue 1232 ASP Chi-restraints excluded: chain P residue 1264 LEU Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14179 Z= 0.267 Angle : 0.592 11.351 19264 Z= 0.312 Chirality : 0.044 0.154 2100 Planarity : 0.004 0.048 2533 Dihedral : 4.919 32.720 1958 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 4.94 % Allowed : 22.43 % Favored : 72.63 % 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: 1775 helix: -1.73 (0.28), residues: 303 sheet: -1.86 (0.21), residues: 541 loop : -2.78 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 228 HIS 0.005 0.001 HIS E 83 PHE 0.037 0.002 PHE A 428 TYR 0.019 0.001 TYR B 345 ARG 0.009 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 170 time to evaluate : 1.553 Fit side-chains REVERT: A 430 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6288 (pt) REVERT: B 215 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6979 (ttp-170) REVERT: B 306 MET cc_start: 0.7236 (mtm) cc_final: 0.6944 (mtp) REVERT: P 1072 GLU cc_start: 0.5433 (mm-30) cc_final: 0.3247 (tp30) REVERT: P 1286 TYR cc_start: 0.4695 (m-80) cc_final: 0.4408 (m-10) outliers start: 72 outliers final: 56 residues processed: 225 average time/residue: 0.2219 time to fit residues: 77.0440 Evaluate side-chains 215 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 157 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain P residue 1019 LEU Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1129 ASP Chi-restraints excluded: chain P residue 1213 SER Chi-restraints excluded: chain P residue 1227 LEU Chi-restraints excluded: chain P residue 1232 ASP Chi-restraints excluded: chain P residue 1264 LEU Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.5980 chunk 154 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 765 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN E 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14179 Z= 0.199 Angle : 0.548 9.397 19264 Z= 0.285 Chirality : 0.043 0.156 2100 Planarity : 0.004 0.047 2533 Dihedral : 4.460 31.081 1958 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.98 % Allowed : 23.66 % Favored : 72.36 % 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: -3.15 (0.19), residues: 1775 helix: -1.37 (0.30), residues: 301 sheet: -1.62 (0.21), residues: 529 loop : -2.66 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 228 HIS 0.004 0.001 HIS E 83 PHE 0.023 0.001 PHE A 440 TYR 0.016 0.001 TYR B 345 ARG 0.010 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 175 time to evaluate : 1.417 Fit side-chains REVERT: A 716 LEU cc_start: 0.8697 (tt) cc_final: 0.8450 (mp) REVERT: B 215 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7021 (ttp-170) REVERT: B 317 TRP cc_start: 0.7216 (p-90) cc_final: 0.6935 (p-90) REVERT: D 207 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7106 (p0) REVERT: P 1072 GLU cc_start: 0.5416 (mm-30) cc_final: 0.2826 (tp30) REVERT: P 1120 ASP cc_start: 0.3647 (m-30) cc_final: 0.2314 (t70) REVERT: P 1264 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.6104 (mt) REVERT: P 1286 TYR cc_start: 0.4652 (m-80) cc_final: 0.4359 (m-10) outliers start: 58 outliers final: 45 residues processed: 218 average time/residue: 0.2423 time to fit residues: 80.2888 Evaluate side-chains 209 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 161 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1213 SER Chi-restraints excluded: chain P residue 1264 LEU Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 0.0770 chunk 19 optimal weight: 0.0670 chunk 97 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14179 Z= 0.140 Angle : 0.512 10.014 19264 Z= 0.264 Chirality : 0.042 0.155 2100 Planarity : 0.003 0.047 2533 Dihedral : 4.082 29.158 1958 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.57 % Allowed : 24.42 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.19), residues: 1775 helix: -1.05 (0.31), residues: 301 sheet: -1.48 (0.21), residues: 556 loop : -2.53 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 228 HIS 0.005 0.001 HIS P1127 PHE 0.017 0.001 PHE A 440 TYR 0.014 0.001 TYR D 110 ARG 0.010 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 174 time to evaluate : 1.576 Fit side-chains REVERT: A 467 THR cc_start: 0.8288 (m) cc_final: 0.8076 (m) REVERT: D 207 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.6962 (p0) REVERT: P 1056 PHE cc_start: 0.3546 (OUTLIER) cc_final: 0.3250 (m-80) REVERT: P 1072 GLU cc_start: 0.5177 (mm-30) cc_final: 0.2596 (tp30) REVERT: P 1120 ASP cc_start: 0.3465 (m-30) cc_final: 0.3234 (m-30) REVERT: P 1264 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.6056 (mt) REVERT: P 1286 TYR cc_start: 0.4544 (m-80) cc_final: 0.4264 (m-10) outliers start: 52 outliers final: 39 residues processed: 212 average time/residue: 0.2244 time to fit residues: 73.1053 Evaluate side-chains 206 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 164 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain P residue 1056 PHE Chi-restraints excluded: chain P residue 1064 GLN Chi-restraints excluded: chain P residue 1129 ASP Chi-restraints excluded: chain P residue 1232 ASP Chi-restraints excluded: chain P residue 1264 LEU Chi-restraints excluded: chain P residue 1288 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS P1064 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14179 Z= 0.153 Angle : 0.514 9.463 19264 Z= 0.265 Chirality : 0.043 0.175 2100 Planarity : 0.003 0.048 2533 Dihedral : 4.018 28.815 1958 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.18 % Allowed : 23.94 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.19), residues: 1775 helix: -0.85 (0.31), residues: 299 sheet: -1.43 (0.21), residues: 556 loop : -2.43 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 228 HIS 0.006 0.001 HIS P1127 PHE 0.023 0.001 PHE A 802 TYR 0.014 0.001 TYR B 345 ARG 0.011 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 168 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 372 MET cc_start: 0.8293 (mmt) cc_final: 0.7954 (mmt) REVERT: B 189 MET cc_start: 0.6353 (tpp) cc_final: 0.6142 (tpp) REVERT: D 207 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.6981 (p0) REVERT: P 1072 GLU cc_start: 0.5126 (mm-30) cc_final: 0.2526 (tp30) REVERT: P 1120 ASP cc_start: 0.3741 (m-30) cc_final: 0.1870 (p0) REVERT: P 1154 GLU cc_start: 0.5497 (tm-30) cc_final: 0.5266 (tm-30) REVERT: P 1264 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.6328 (mt) REVERT: P 1286 TYR cc_start: 0.4588 (m-80) cc_final: 0.4296 (m-10) outliers start: 61 outliers final: 52 residues processed: 211 average time/residue: 0.2268 time to fit residues: 73.2985 Evaluate side-chains 219 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 165 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain P residue 1046 MET Chi-restraints excluded: chain P residue 1056 PHE Chi-restraints excluded: chain P residue 1064 GLN Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1213 SER Chi-restraints excluded: chain P residue 1232 ASP Chi-restraints excluded: chain P residue 1264 LEU Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 chunk 158 optimal weight: 10.0000 chunk 95 optimal weight: 0.4980 chunk 69 optimal weight: 0.0070 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 64 HIS ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1064 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14179 Z= 0.252 Angle : 0.573 11.293 19264 Z= 0.298 Chirality : 0.044 0.160 2100 Planarity : 0.004 0.052 2533 Dihedral : 4.380 30.234 1958 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 4.39 % Allowed : 24.01 % Favored : 71.60 % 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: -2.83 (0.19), residues: 1775 helix: -0.93 (0.31), residues: 300 sheet: -1.46 (0.21), residues: 558 loop : -2.51 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 228 HIS 0.005 0.001 HIS P1127 PHE 0.023 0.002 PHE A 802 TYR 0.015 0.001 TYR B 345 ARG 0.011 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 164 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: A 276 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7316 (p0) REVERT: A 646 MET cc_start: 0.8070 (tpt) cc_final: 0.7371 (tpt) REVERT: D 58 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6419 (mp) REVERT: D 207 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7238 (p0) REVERT: P 1072 GLU cc_start: 0.5427 (mm-30) cc_final: 0.3230 (tp30) REVERT: P 1120 ASP cc_start: 0.3975 (m-30) cc_final: 0.1951 (p0) REVERT: P 1194 MET cc_start: 0.2910 (ttt) cc_final: 0.2695 (ttm) REVERT: P 1264 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7189 (tp) REVERT: P 1286 TYR cc_start: 0.4691 (m-80) cc_final: 0.4395 (m-10) outliers start: 64 outliers final: 53 residues processed: 210 average time/residue: 0.2276 time to fit residues: 73.5449 Evaluate side-chains 214 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 157 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain P residue 1056 PHE Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1208 VAL Chi-restraints excluded: chain P residue 1213 SER Chi-restraints excluded: chain P residue 1227 LEU Chi-restraints excluded: chain P residue 1232 ASP Chi-restraints excluded: chain P residue 1264 LEU Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS E 34 GLN P1064 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14179 Z= 0.407 Angle : 0.690 13.542 19264 Z= 0.362 Chirality : 0.048 0.220 2100 Planarity : 0.004 0.053 2533 Dihedral : 5.198 33.254 1958 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 4.25 % Allowed : 24.42 % Favored : 71.33 % 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: -3.18 (0.19), residues: 1775 helix: -1.20 (0.30), residues: 299 sheet: -1.76 (0.21), residues: 559 loop : -2.68 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 48 HIS 0.006 0.002 HIS P1062 PHE 0.027 0.002 PHE A 791 TYR 0.020 0.002 TYR B 345 ARG 0.012 0.001 ARG B 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 155 time to evaluate : 1.661 Fit side-chains REVERT: B 140 THR cc_start: 0.6402 (m) cc_final: 0.6107 (t) REVERT: B 191 SER cc_start: 0.8277 (t) cc_final: 0.7851 (p) REVERT: D 58 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6488 (mp) REVERT: P 1056 PHE cc_start: 0.3488 (OUTLIER) cc_final: 0.2744 (m-10) REVERT: P 1072 GLU cc_start: 0.5621 (mm-30) cc_final: 0.3558 (tp30) REVERT: P 1264 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7318 (tp) REVERT: P 1286 TYR cc_start: 0.4435 (m-80) cc_final: 0.4220 (m-10) outliers start: 62 outliers final: 51 residues processed: 200 average time/residue: 0.2290 time to fit residues: 71.2320 Evaluate side-chains 202 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 148 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain P residue 1056 PHE Chi-restraints excluded: chain P residue 1064 GLN Chi-restraints excluded: chain P residue 1103 VAL Chi-restraints excluded: chain P residue 1213 SER Chi-restraints excluded: chain P residue 1227 LEU Chi-restraints excluded: chain P residue 1232 ASP Chi-restraints excluded: chain P residue 1264 LEU Chi-restraints excluded: chain P residue 1288 VAL Chi-restraints excluded: chain P residue 1300 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1064 GLN P1127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.209845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.163023 restraints weight = 15340.992| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.02 r_work: 0.3710 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 14179 Z= 0.358 Angle : 0.896 59.159 19264 Z= 0.500 Chirality : 0.046 0.192 2100 Planarity : 0.004 0.050 2533 Dihedral : 5.196 33.239 1958 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 4.39 % Allowed : 24.69 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.19 (0.19), residues: 1775 helix: -1.21 (0.30), residues: 299 sheet: -1.74 (0.21), residues: 557 loop : -2.71 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 48 HIS 0.006 0.001 HIS B 324 PHE 0.026 0.002 PHE A 791 TYR 0.018 0.002 TYR B 345 ARG 0.010 0.001 ARG B 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3158.70 seconds wall clock time: 57 minutes 50.40 seconds (3470.40 seconds total)