Starting phenix.real_space_refine on Wed Feb 14 08:19:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1i_30048/02_2024/6m1i_30048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1i_30048/02_2024/6m1i_30048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1i_30048/02_2024/6m1i_30048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1i_30048/02_2024/6m1i_30048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1i_30048/02_2024/6m1i_30048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1i_30048/02_2024/6m1i_30048.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5682 2.51 5 N 1537 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 50": "OE1" <-> "OE2" Residue "F GLU 309": "OE1" <-> "OE2" Residue "F GLU 322": "OE1" <-> "OE2" Residue "F GLU 330": "OE1" <-> "OE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 374": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8916 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2841 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 339} Chain breaks: 4 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "C" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2595 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1862 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.14, per 1000 atoms: 0.58 Number of scatterers: 8916 At special positions: 0 Unit cell: (84.007, 105.827, 153.831, 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 58 16.00 O 1639 8.00 N 1537 7.00 C 5682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 63 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 118 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 296 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 107 " distance=2.02 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: 3.36 Conformation dependent library (CDL) restraints added in 1.8 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 39.1% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 25 through 41 removed outlier: 4.274A pdb=" N GLN A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 87 through 111 removed outlier: 3.504A pdb=" N MET A 111 " --> pdb=" O ASP A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 111' Processing helix chain 'A' and resid 129 through 135 removed outlier: 3.573A pdb=" N CYS A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 170 removed outlier: 4.044A pdb=" N TYR A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.675A pdb=" N ILE A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS A 176 " --> pdb=" O MET A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 176' Processing helix chain 'A' and resid 185 through 209 removed outlier: 3.580A pdb=" N MET A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASN A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 removed outlier: 3.536A pdb=" N HIS A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 4.279A pdb=" N MET A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 254 removed outlier: 3.622A pdb=" N GLY A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 286 removed outlier: 3.756A pdb=" N TYR A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 271 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE A 272 " --> pdb=" O TRP A 268 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Proline residue: A 277 - end of helix removed outlier: 3.712A pdb=" N PHE A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.667A pdb=" N VAL A 308 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 329 removed outlier: 4.101A pdb=" N SER A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.586A pdb=" N GLY A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.606A pdb=" N VAL A 368 " --> pdb=" O HIS A 365 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 369 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 removed outlier: 3.615A pdb=" N LYS A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 388 removed outlier: 3.685A pdb=" N PHE A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 400 removed outlier: 3.821A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 419 removed outlier: 3.584A pdb=" N LYS A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 removed outlier: 3.670A pdb=" N SER B 11 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.865A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.594A pdb=" N LYS C 65 " --> pdb=" O GLY C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.575A pdb=" N ASP C 90 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.504A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.773A pdb=" N ASP D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 26 removed outlier: 3.526A pdb=" N ARG E 22 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.657A pdb=" N ILE E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 38 removed outlier: 3.786A pdb=" N ALA F 18 " --> pdb=" O ASN F 14 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN F 23 " --> pdb=" O GLN F 19 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN F 29 " --> pdb=" O LYS F 25 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN F 35 " --> pdb=" O GLN F 31 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL F 36 " --> pdb=" O LYS F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 59 removed outlier: 3.550A pdb=" N ASN F 54 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE F 56 " --> pdb=" O GLY F 52 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL F 57 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS F 58 " --> pdb=" O ASN F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 278 removed outlier: 3.689A pdb=" N SER F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.601A pdb=" N GLU F 299 " --> pdb=" O ASP F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 350 removed outlier: 3.749A pdb=" N ARG F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE F 348 " --> pdb=" O GLU F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 390 removed outlier: 4.015A pdb=" N ASP F 381 " --> pdb=" O ASN F 377 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE F 383 " --> pdb=" O CYS F 379 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 76 removed outlier: 4.428A pdb=" N VAL A 75 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 114 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.552A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.521A pdb=" N SER C 59 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 124 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 46 through 51 removed outlier: 6.672A pdb=" N ILE E 338 " --> pdb=" O ARG E 48 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR E 50 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU E 336 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA E 328 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU E 318 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY E 330 " --> pdb=" O SER E 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 58 through 62 removed outlier: 3.560A pdb=" N ALA E 60 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS E 91 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP E 83 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS E 89 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 100 through 105 removed outlier: 3.697A pdb=" N ARG E 137 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN E 125 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL E 135 " --> pdb=" O ASN E 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 146 through 151 removed outlier: 3.979A pdb=" N ILE E 157 " --> pdb=" O TRP E 169 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS E 166 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR E 179 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU E 168 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN E 175 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 187 through 192 removed outlier: 6.855A pdb=" N GLY E 202 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU E 190 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL E 200 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE E 199 " --> pdb=" O TRP E 211 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 203 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA E 208 " --> pdb=" O THR E 221 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR E 221 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU E 210 " --> pdb=" O ARG E 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 229 through 234 removed outlier: 3.820A pdb=" N MET E 262 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP E 254 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU E 260 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 275 through 278 removed outlier: 3.806A pdb=" N SER E 275 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP E 298 " --> pdb=" O ARG E 304 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ARG E 304 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 207 through 214 removed outlier: 4.370A pdb=" N VAL F 224 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 9.564A pdb=" N ALA F 243 " --> pdb=" O THR F 40 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ARG F 42 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE F 245 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU F 44 " --> pdb=" O ILE F 245 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE F 244 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE F 290 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE F 246 " --> pdb=" O PHE F 290 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 951 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: 2.81 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2643 1.33 - 1.45: 2009 1.45 - 1.58: 4382 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 9114 Sorted by residual: bond pdb=" N PHE A 402 " pdb=" CA PHE A 402 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.20e-02 6.94e+03 7.29e+00 bond pdb=" N TYR A 400 " pdb=" CA TYR A 400 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.29e-02 6.01e+03 6.16e+00 bond pdb=" N GLU A 247 " pdb=" CA GLU A 247 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.17e+00 bond pdb=" N ARG A 379 " pdb=" CA ARG A 379 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.15e-02 7.56e+03 4.20e+00 bond pdb=" N ARG A 263 " pdb=" CA ARG A 263 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.33e-02 5.65e+03 3.81e+00 ... (remaining 9109 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.14: 119 105.14 - 112.38: 4433 112.38 - 119.61: 3254 119.61 - 126.85: 4402 126.85 - 134.08: 137 Bond angle restraints: 12345 Sorted by residual: angle pdb=" N ARG A 263 " pdb=" CA ARG A 263 " pdb=" C ARG A 263 " ideal model delta sigma weight residual 113.28 105.28 8.00 1.22e+00 6.72e-01 4.31e+01 angle pdb=" C TYR A 400 " pdb=" N CYS A 401 " pdb=" CA CYS A 401 " ideal model delta sigma weight residual 122.79 114.01 8.78 1.70e+00 3.46e-01 2.67e+01 angle pdb=" N ILE A 309 " pdb=" CA ILE A 309 " pdb=" C ILE A 309 " ideal model delta sigma weight residual 111.56 107.22 4.34 8.60e-01 1.35e+00 2.55e+01 angle pdb=" C LYS C 76 " pdb=" N ASN C 77 " pdb=" CA ASN C 77 " ideal model delta sigma weight residual 122.46 129.04 -6.58 1.41e+00 5.03e-01 2.18e+01 angle pdb=" C SER A 302 " pdb=" N THR A 303 " pdb=" CA THR A 303 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 ... (remaining 12340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4728 17.77 - 35.53: 546 35.53 - 53.30: 82 53.30 - 71.07: 23 71.07 - 88.84: 6 Dihedral angle restraints: 5385 sinusoidal: 2116 harmonic: 3269 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 118 " pdb=" CB CYS A 118 " ideal model delta sinusoidal sigma weight residual -86.00 -144.22 58.22 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CA PHE A 127 " pdb=" C PHE A 127 " pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta harmonic sigma weight residual 180.00 146.56 33.44 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA THR C 114 " pdb=" C THR C 114 " pdb=" N TYR C 115 " pdb=" CA TYR C 115 " ideal model delta harmonic sigma weight residual 180.00 148.82 31.18 0 5.00e+00 4.00e-02 3.89e+01 ... (remaining 5382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 968 0.058 - 0.117: 314 0.117 - 0.175: 70 0.175 - 0.233: 7 0.233 - 0.292: 5 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CB VAL F 241 " pdb=" CA VAL F 241 " pdb=" CG1 VAL F 241 " pdb=" CG2 VAL F 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE A 221 " pdb=" CA ILE A 221 " pdb=" CG1 ILE A 221 " pdb=" CG2 ILE A 221 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB THR C 91 " pdb=" CA THR C 91 " pdb=" OG1 THR C 91 " pdb=" CG2 THR C 91 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 1361 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 311 " 0.056 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO A 312 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 235 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO E 236 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 87 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.15e+00 pdb=" N PRO C 88 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 88 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 88 " -0.031 5.00e-02 4.00e+02 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1376 2.75 - 3.29: 8293 3.29 - 3.82: 14927 3.82 - 4.36: 17396 4.36 - 4.90: 29175 Nonbonded interactions: 71167 Sorted by model distance: nonbonded pdb=" ND1 HIS A 189 " pdb=" OE2 GLU A 247 " model vdw 2.210 2.520 nonbonded pdb=" OG SER E 245 " pdb=" OD1 ASP E 247 " model vdw 2.222 2.440 nonbonded pdb=" OH TYR A 150 " pdb=" OG SER B 9 " model vdw 2.274 2.440 nonbonded pdb=" O ARG C 98 " pdb=" OH TYR C 115 " model vdw 2.283 2.440 nonbonded pdb=" O THR C 111 " pdb=" NH2 ARG C 118 " model vdw 2.299 2.520 ... (remaining 71162 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 1.800 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.620 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 : 0.008 0.076 9114 Z= 0.516 Angle : 0.968 12.046 12345 Z= 0.554 Chirality : 0.061 0.292 1364 Planarity : 0.007 0.086 1574 Dihedral : 15.399 88.836 3258 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.32 % Allowed : 12.61 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.09 % 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: -4.80 (0.20), residues: 1102 helix: -4.08 (0.13), residues: 400 sheet: -1.74 (0.34), residues: 229 loop : -2.96 (0.23), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP F 234 HIS 0.013 0.002 HIS F 357 PHE 0.024 0.003 PHE E 241 TYR 0.030 0.003 TYR E 105 ARG 0.005 0.001 ARG F 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 LEU cc_start: 0.8332 (tt) cc_final: 0.7946 (tp) REVERT: B 3 ASP cc_start: 0.8810 (m-30) cc_final: 0.8562 (m-30) REVERT: B 12 ARG cc_start: 0.8951 (ttp-170) cc_final: 0.8239 (ttp-110) REVERT: B 14 ARG cc_start: 0.9146 (tpp80) cc_final: 0.8920 (tpp80) REVERT: C 19 ARG cc_start: 0.7997 (ppt170) cc_final: 0.7761 (ppt170) REVERT: C 20 LEU cc_start: 0.8164 (mt) cc_final: 0.7883 (mm) REVERT: C 33 LYS cc_start: 0.8316 (tttt) cc_final: 0.8108 (ttmt) REVERT: C 83 MET cc_start: 0.8713 (mtm) cc_final: 0.8051 (mtm) REVERT: E 8 ARG cc_start: 0.7593 (ttt180) cc_final: 0.7214 (tpm170) REVERT: E 118 ASP cc_start: 0.8325 (p0) cc_final: 0.8021 (p0) REVERT: F 221 MET cc_start: 0.7727 (ttp) cc_final: 0.7372 (ttp) REVERT: F 342 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8283 (ttp80) REVERT: F 386 MET cc_start: 0.7687 (tmm) cc_final: 0.7468 (tpp) outliers start: 3 outliers final: 3 residues processed: 190 average time/residue: 0.2884 time to fit residues: 70.1297 Evaluate side-chains 135 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 392 GLN A 404 ASN C 31 ASN E 88 ASN F 19 GLN F 41 HIS F 54 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 GLN F 292 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9114 Z= 0.184 Angle : 0.602 7.346 12345 Z= 0.329 Chirality : 0.044 0.193 1364 Planarity : 0.005 0.049 1574 Dihedral : 6.085 32.437 1229 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.31 % Allowed : 18.70 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.22), residues: 1102 helix: -2.30 (0.21), residues: 409 sheet: -1.16 (0.34), residues: 226 loop : -2.49 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 243 HIS 0.004 0.001 HIS F 357 PHE 0.026 0.002 PHE F 222 TYR 0.019 0.001 TYR A 157 ARG 0.005 0.000 ARG F 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.5211 (pm20) REVERT: A 225 GLU cc_start: 0.6463 (tt0) cc_final: 0.6160 (tp30) REVERT: C 18 LEU cc_start: 0.8898 (tp) cc_final: 0.8528 (tt) REVERT: C 20 LEU cc_start: 0.8374 (mt) cc_final: 0.8023 (mt) REVERT: C 83 MET cc_start: 0.8562 (mtm) cc_final: 0.8202 (mtp) REVERT: C 125 THR cc_start: 0.8249 (p) cc_final: 0.7932 (p) REVERT: D 18 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8436 (tp40) REVERT: F 222 PHE cc_start: 0.7962 (m-80) cc_final: 0.7762 (m-80) outliers start: 22 outliers final: 13 residues processed: 174 average time/residue: 0.2550 time to fit residues: 58.2625 Evaluate side-chains 152 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 6.9990 chunk 30 optimal weight: 0.0770 chunk 82 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN C 123 GLN E 183 HIS E 311 HIS F 23 ASN F 390 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9114 Z= 0.235 Angle : 0.615 6.976 12345 Z= 0.331 Chirality : 0.044 0.201 1364 Planarity : 0.004 0.050 1574 Dihedral : 5.667 26.414 1226 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.10 % Allowed : 20.90 % Favored : 75.00 % 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: -2.64 (0.23), residues: 1102 helix: -1.48 (0.23), residues: 420 sheet: -0.83 (0.34), residues: 225 loop : -2.39 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 243 HIS 0.006 0.001 HIS F 220 PHE 0.014 0.002 PHE F 376 TYR 0.020 0.001 TYR A 211 ARG 0.007 0.000 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 152 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.5907 (OUTLIER) cc_final: 0.5314 (pm20) REVERT: A 225 GLU cc_start: 0.6464 (tt0) cc_final: 0.6165 (tp30) REVERT: A 230 MET cc_start: 0.8572 (tpp) cc_final: 0.8364 (tpt) REVERT: C 18 LEU cc_start: 0.8775 (tp) cc_final: 0.8574 (tp) REVERT: C 20 LEU cc_start: 0.8455 (mt) cc_final: 0.8197 (mt) REVERT: C 83 MET cc_start: 0.8542 (mtm) cc_final: 0.8053 (mtm) REVERT: F 13 ARG cc_start: 0.8924 (mtt180) cc_final: 0.8677 (mpp80) REVERT: F 220 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.6616 (t-90) REVERT: F 342 ARG cc_start: 0.8791 (tmm-80) cc_final: 0.8420 (tmm-80) outliers start: 39 outliers final: 25 residues processed: 177 average time/residue: 0.2402 time to fit residues: 56.9537 Evaluate side-chains 158 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 66 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN C 31 ASN E 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9114 Z= 0.154 Angle : 0.570 7.783 12345 Z= 0.300 Chirality : 0.043 0.180 1364 Planarity : 0.004 0.041 1574 Dihedral : 5.162 22.862 1226 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.15 % Allowed : 22.37 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.24), residues: 1102 helix: -0.97 (0.25), residues: 419 sheet: -0.55 (0.35), residues: 221 loop : -2.16 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 297 HIS 0.004 0.001 HIS F 220 PHE 0.010 0.001 PHE F 376 TYR 0.024 0.001 TYR A 211 ARG 0.009 0.000 ARG F 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 LEU cc_start: 0.8979 (tp) cc_final: 0.8576 (tt) REVERT: C 12 VAL cc_start: 0.8562 (t) cc_final: 0.8331 (m) REVERT: C 20 LEU cc_start: 0.8420 (mt) cc_final: 0.8127 (mt) REVERT: C 34 MET cc_start: 0.7977 (mtp) cc_final: 0.7763 (mtt) REVERT: C 67 ARG cc_start: 0.7427 (ptp90) cc_final: 0.7068 (ptp90) REVERT: C 83 MET cc_start: 0.8568 (mtm) cc_final: 0.8122 (mtm) REVERT: D 18 GLN cc_start: 0.8952 (tp-100) cc_final: 0.8515 (tp40) REVERT: E 217 MET cc_start: 0.7499 (ppp) cc_final: 0.7137 (ppp) REVERT: E 241 PHE cc_start: 0.9054 (p90) cc_final: 0.8642 (p90) REVERT: F 13 ARG cc_start: 0.8951 (mtt180) cc_final: 0.8703 (mpp80) REVERT: F 220 HIS cc_start: 0.7448 (OUTLIER) cc_final: 0.6352 (t-90) REVERT: F 342 ARG cc_start: 0.8725 (tmm-80) cc_final: 0.8423 (tmm-80) outliers start: 30 outliers final: 20 residues processed: 178 average time/residue: 0.2498 time to fit residues: 59.6500 Evaluate side-chains 162 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 0.3980 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 311 HIS ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9114 Z= 0.260 Angle : 0.615 7.247 12345 Z= 0.324 Chirality : 0.044 0.179 1364 Planarity : 0.004 0.040 1574 Dihedral : 5.239 27.720 1226 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.52 % Allowed : 21.95 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.24), residues: 1102 helix: -0.72 (0.25), residues: 423 sheet: -0.40 (0.36), residues: 219 loop : -2.19 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 211 HIS 0.005 0.001 HIS F 357 PHE 0.016 0.002 PHE F 376 TYR 0.013 0.001 TYR A 157 ARG 0.004 0.000 ARG F 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7965 (pt0) cc_final: 0.7651 (pm20) REVERT: A 230 MET cc_start: 0.8627 (tpt) cc_final: 0.8320 (tpp) REVERT: C 20 LEU cc_start: 0.8418 (mt) cc_final: 0.8153 (mt) REVERT: C 34 MET cc_start: 0.8039 (mtp) cc_final: 0.7815 (mtt) REVERT: C 83 MET cc_start: 0.8628 (mtm) cc_final: 0.8187 (mtm) REVERT: D 18 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8546 (tp40) REVERT: E 8 ARG cc_start: 0.8726 (mtt180) cc_final: 0.8105 (tpm170) REVERT: E 217 MET cc_start: 0.7347 (ppp) cc_final: 0.7094 (ppp) REVERT: F 13 ARG cc_start: 0.9053 (mtt180) cc_final: 0.8759 (mpp80) REVERT: F 342 ARG cc_start: 0.8718 (tmm-80) cc_final: 0.8406 (tmm-80) outliers start: 43 outliers final: 34 residues processed: 172 average time/residue: 0.2336 time to fit residues: 54.1535 Evaluate side-chains 172 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.0070 chunk 55 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN E 183 HIS ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9114 Z= 0.155 Angle : 0.565 7.426 12345 Z= 0.294 Chirality : 0.042 0.179 1364 Planarity : 0.003 0.039 1574 Dihedral : 4.844 22.922 1226 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.26 % Allowed : 23.63 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.25), residues: 1102 helix: -0.35 (0.26), residues: 421 sheet: -0.23 (0.36), residues: 210 loop : -1.97 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 297 HIS 0.003 0.001 HIS F 357 PHE 0.012 0.001 PHE F 376 TYR 0.024 0.001 TYR A 211 ARG 0.004 0.000 ARG F 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7922 (pt0) cc_final: 0.7612 (pm20) REVERT: A 165 LEU cc_start: 0.8968 (tp) cc_final: 0.8608 (tt) REVERT: A 197 MET cc_start: 0.8476 (mtt) cc_final: 0.8025 (mtt) REVERT: C 20 LEU cc_start: 0.8353 (mt) cc_final: 0.8058 (mt) REVERT: C 34 MET cc_start: 0.8068 (mtp) cc_final: 0.7814 (mtt) REVERT: C 83 MET cc_start: 0.8560 (mtm) cc_final: 0.8125 (mtm) REVERT: D 18 GLN cc_start: 0.8959 (tp-100) cc_final: 0.8573 (tp40) REVERT: D 20 LYS cc_start: 0.8335 (tmmt) cc_final: 0.7711 (tmmt) REVERT: E 217 MET cc_start: 0.7419 (ppp) cc_final: 0.7205 (ppp) REVERT: F 13 ARG cc_start: 0.8984 (mtt180) cc_final: 0.8726 (mpp80) REVERT: F 342 ARG cc_start: 0.8711 (tmm-80) cc_final: 0.8407 (tmm-80) REVERT: F 350 THR cc_start: 0.8418 (p) cc_final: 0.8184 (p) outliers start: 31 outliers final: 27 residues processed: 181 average time/residue: 0.2282 time to fit residues: 55.8575 Evaluate side-chains 168 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 349 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 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 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN E 183 HIS ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9114 Z= 0.318 Angle : 0.656 9.213 12345 Z= 0.344 Chirality : 0.045 0.196 1364 Planarity : 0.004 0.040 1574 Dihedral : 5.232 29.939 1226 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.94 % Allowed : 23.42 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.25), residues: 1102 helix: -0.40 (0.25), residues: 422 sheet: -0.26 (0.35), residues: 224 loop : -2.03 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 211 HIS 0.007 0.001 HIS F 220 PHE 0.021 0.002 PHE F 376 TYR 0.014 0.002 TYR F 318 ARG 0.003 0.000 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 131 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7975 (pt0) cc_final: 0.7625 (pm20) REVERT: A 230 MET cc_start: 0.8265 (tpp) cc_final: 0.7658 (tpp) REVERT: C 3 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6563 (pm20) REVERT: C 20 LEU cc_start: 0.8375 (mt) cc_final: 0.8091 (mt) REVERT: C 34 MET cc_start: 0.8069 (mtp) cc_final: 0.7780 (mtt) REVERT: C 83 MET cc_start: 0.8609 (mtm) cc_final: 0.8219 (mtm) REVERT: D 18 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8555 (tp40) REVERT: F 13 ARG cc_start: 0.9067 (mtt180) cc_final: 0.8763 (mpp80) outliers start: 47 outliers final: 38 residues processed: 166 average time/residue: 0.2303 time to fit residues: 52.0957 Evaluate side-chains 168 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 0.0370 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN E 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9114 Z= 0.206 Angle : 0.605 8.399 12345 Z= 0.315 Chirality : 0.044 0.173 1364 Planarity : 0.003 0.039 1574 Dihedral : 5.037 26.461 1226 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.52 % Allowed : 24.26 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1102 helix: -0.22 (0.26), residues: 421 sheet: -0.21 (0.35), residues: 224 loop : -1.91 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 243 HIS 0.003 0.001 HIS F 357 PHE 0.013 0.001 PHE A 362 TYR 0.022 0.001 TYR A 211 ARG 0.003 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 137 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7966 (pt0) cc_final: 0.7639 (pm20) REVERT: C 20 LEU cc_start: 0.8382 (mt) cc_final: 0.8179 (mt) REVERT: C 34 MET cc_start: 0.8086 (mtp) cc_final: 0.7789 (mtt) REVERT: C 83 MET cc_start: 0.8607 (mtm) cc_final: 0.8196 (mpp) REVERT: D 18 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8555 (tp40) REVERT: E 217 MET cc_start: 0.7795 (ppp) cc_final: 0.7541 (ppp) REVERT: F 13 ARG cc_start: 0.9055 (mtt180) cc_final: 0.8763 (mpp80) REVERT: F 318 TYR cc_start: 0.7914 (t80) cc_final: 0.7425 (t80) REVERT: F 350 THR cc_start: 0.8476 (p) cc_final: 0.8248 (p) outliers start: 43 outliers final: 36 residues processed: 169 average time/residue: 0.2252 time to fit residues: 51.9820 Evaluate side-chains 172 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN E 183 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9114 Z= 0.278 Angle : 0.630 8.516 12345 Z= 0.331 Chirality : 0.045 0.187 1364 Planarity : 0.004 0.039 1574 Dihedral : 5.133 27.872 1226 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.73 % Allowed : 23.95 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1102 helix: -0.17 (0.26), residues: 421 sheet: -0.21 (0.35), residues: 224 loop : -1.96 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 211 HIS 0.005 0.001 HIS F 220 PHE 0.017 0.002 PHE F 376 TYR 0.015 0.001 TYR F 318 ARG 0.004 0.000 ARG F 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 134 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7955 (pt0) cc_final: 0.7609 (pm20) REVERT: A 230 MET cc_start: 0.8254 (tpp) cc_final: 0.7647 (tpp) REVERT: C 20 LEU cc_start: 0.8386 (mt) cc_final: 0.8103 (mt) REVERT: C 34 MET cc_start: 0.8094 (mtp) cc_final: 0.7780 (mtt) REVERT: C 83 MET cc_start: 0.8617 (mtm) cc_final: 0.8144 (mtm) REVERT: D 18 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8538 (tp40) REVERT: E 217 MET cc_start: 0.7840 (ppp) cc_final: 0.7557 (ppp) REVERT: F 13 ARG cc_start: 0.9066 (mtt180) cc_final: 0.8766 (mpp80) REVERT: F 318 TYR cc_start: 0.7920 (t80) cc_final: 0.7421 (t80) outliers start: 45 outliers final: 42 residues processed: 166 average time/residue: 0.2220 time to fit residues: 50.3453 Evaluate side-chains 175 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 133 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 35 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 0.0000 chunk 68 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN E 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9114 Z= 0.162 Angle : 0.591 8.166 12345 Z= 0.307 Chirality : 0.043 0.189 1364 Planarity : 0.003 0.038 1574 Dihedral : 4.857 23.445 1226 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.57 % Allowed : 25.21 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.25), residues: 1102 helix: -0.01 (0.26), residues: 421 sheet: -0.12 (0.36), residues: 215 loop : -1.81 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 243 HIS 0.003 0.001 HIS F 362 PHE 0.010 0.001 PHE A 362 TYR 0.024 0.001 TYR A 211 ARG 0.007 0.000 ARG F 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8172 (tpp) cc_final: 0.7594 (tpp) REVERT: C 20 LEU cc_start: 0.8339 (mt) cc_final: 0.8134 (mt) REVERT: C 34 MET cc_start: 0.8070 (mtp) cc_final: 0.7812 (mtt) REVERT: C 83 MET cc_start: 0.8653 (mtm) cc_final: 0.8236 (mpp) REVERT: D 18 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8601 (tp40) REVERT: E 217 MET cc_start: 0.7895 (ppp) cc_final: 0.7565 (ppp) REVERT: E 340 ASN cc_start: 0.7840 (t0) cc_final: 0.7290 (t0) REVERT: F 13 ARG cc_start: 0.9049 (mtt180) cc_final: 0.8763 (mpp80) REVERT: F 318 TYR cc_start: 0.7790 (t80) cc_final: 0.7366 (t80) REVERT: F 342 ARG cc_start: 0.8676 (tmm-80) cc_final: 0.8254 (tmm-80) REVERT: F 350 THR cc_start: 0.8442 (p) cc_final: 0.8212 (p) outliers start: 34 outliers final: 33 residues processed: 167 average time/residue: 0.2202 time to fit residues: 50.2781 Evaluate side-chains 170 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain F residue 220 HIS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 349 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN E 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.092889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.070407 restraints weight = 26534.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.072568 restraints weight = 14003.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073980 restraints weight = 9550.005| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9114 Z= 0.224 Angle : 0.604 8.384 12345 Z= 0.315 Chirality : 0.044 0.189 1364 Planarity : 0.003 0.038 1574 Dihedral : 4.889 25.379 1226 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.99 % Allowed : 25.00 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.25), residues: 1102 helix: 0.00 (0.26), residues: 422 sheet: -0.12 (0.35), residues: 223 loop : -1.86 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 82 HIS 0.005 0.001 HIS E 54 PHE 0.014 0.001 PHE F 376 TYR 0.012 0.001 TYR A 157 ARG 0.006 0.000 ARG F 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2093.94 seconds wall clock time: 38 minutes 46.46 seconds (2326.46 seconds total)