Starting phenix.real_space_refine on Sun Dec 10 17:58:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/12_2023/6ysz_10911.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/12_2023/6ysz_10911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/12_2023/6ysz_10911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/12_2023/6ysz_10911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/12_2023/6ysz_10911.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/12_2023/6ysz_10911.pdb" } resolution = 3.6 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= 0.007 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 60 5.16 5 C 9348 2.51 5 N 2742 2.21 5 O 3042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ARG 130": "NH1" <-> "NH2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 142": "NH1" <-> "NH2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 130": "NH1" <-> "NH2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E ARG 139": "NH1" <-> "NH2" Residue "E ARG 142": "NH1" <-> "NH2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E ARG 279": "NH1" <-> "NH2" Residue "E GLU 307": "OE1" <-> "OE2" Residue "E ARG 310": "NH1" <-> "NH2" Residue "E GLU 320": "OE1" <-> "OE2" Residue "E ARG 323": "NH1" <-> "NH2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 130": "NH1" <-> "NH2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F ARG 142": "NH1" <-> "NH2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "F ARG 310": "NH1" <-> "NH2" Residue "F GLU 320": "OE1" <-> "OE2" Residue "F ARG 323": "NH1" <-> "NH2" Residue "F GLU 335": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15192 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "B" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "C" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "D" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "E" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "F" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Time building chain proxies: 8.13, per 1000 atoms: 0.54 Number of scatterers: 15192 At special positions: 0 Unit cell: (101.15, 97.75, 143.65, 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 60 16.00 O 3042 8.00 N 2742 7.00 C 9348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 3.0 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 6 sheets defined 81.1% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.519A pdb=" N ARG A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 154 Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 282' Processing helix chain 'A' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE A 299 " --> pdb=" O GLN A 295 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 88 removed outlier: 3.722A pdb=" N ASN B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 110 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 154 Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN B 164 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 205 Processing helix chain 'B' and resid 216 through 231 Processing helix chain 'B' and resid 238 through 253 removed outlier: 4.346A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.638A pdb=" N ILE B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 282' Processing helix chain 'B' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 302 " --> pdb=" O GLN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA B 325 " --> pdb=" O ASP B 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'C' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 65 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN C 88 " --> pdb=" O ARG C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 110 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 154 Processing helix chain 'C' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 205 Processing helix chain 'C' and resid 216 through 231 Processing helix chain 'C' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE C 299 " --> pdb=" O GLN C 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 302 " --> pdb=" O GLN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA C 325 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'D' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP D 65 " --> pdb=" O GLN D 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 154 Processing helix chain 'D' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 200 " --> pdb=" O MET D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 205 Processing helix chain 'D' and resid 216 through 231 Processing helix chain 'D' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.709A pdb=" N PHE D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE D 282 " --> pdb=" O TYR D 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 282' Processing helix chain 'D' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP D 302 " --> pdb=" O GLN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 318 removed outlier: 3.640A pdb=" N ASN D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA D 325 " --> pdb=" O ASP D 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA D 371 " --> pdb=" O THR D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP E 65 " --> pdb=" O GLN E 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN E 88 " --> pdb=" O ARG E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 126 removed outlier: 3.503A pdb=" N MET E 101 " --> pdb=" O ASP E 97 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG E 110 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA E 112 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 154 Processing helix chain 'E' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN E 164 " --> pdb=" O ASP E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL E 200 " --> pdb=" O MET E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 205 Processing helix chain 'E' and resid 216 through 231 Processing helix chain 'E' and resid 238 through 253 removed outlier: 4.346A pdb=" N GLN E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.638A pdb=" N ILE E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 278 through 282' Processing helix chain 'E' and resid 283 through 302 removed outlier: 4.530A pdb=" N GLN E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE E 299 " --> pdb=" O GLN E 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP E 302 " --> pdb=" O GLN E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA E 325 " --> pdb=" O ASP E 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU E 327 " --> pdb=" O ARG E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 340 No H-bonds generated for 'chain 'E' and resid 338 through 340' Processing helix chain 'E' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA E 371 " --> pdb=" O THR E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 374 No H-bonds generated for 'chain 'E' and resid 372 through 374' Processing helix chain 'F' and resid 60 through 78 removed outlier: 3.520A pdb=" N ARG F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 65 " --> pdb=" O GLN F 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN F 88 " --> pdb=" O ARG F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET F 101 " --> pdb=" O ASP F 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG F 110 " --> pdb=" O VAL F 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA F 112 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU F 126 " --> pdb=" O GLN F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 154 Processing helix chain 'F' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG F 199 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL F 200 " --> pdb=" O MET F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 205 Processing helix chain 'F' and resid 216 through 231 Processing helix chain 'F' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE F 282 " --> pdb=" O TYR F 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 278 through 282' Processing helix chain 'F' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE F 299 " --> pdb=" O GLN F 295 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP F 302 " --> pdb=" O GLN F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN F 306 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA F 325 " --> pdb=" O ASP F 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA F 371 " --> pdb=" O THR F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing sheet with id=AA1, first strand: chain 'A' and resid 268 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 268 through 270 Processing sheet with id=AA3, first strand: chain 'C' and resid 268 through 270 Processing sheet with id=AA4, first strand: chain 'D' and resid 268 through 270 Processing sheet with id=AA5, first strand: chain 'E' and resid 268 through 270 Processing sheet with id=AA6, first strand: chain 'F' and resid 268 through 270 1021 hydrogen bonds defined for protein. 3045 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: 4.55 Time building geometry restraints manager: 6.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5418 1.34 - 1.46: 1718 1.46 - 1.57: 8158 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 15414 Sorted by residual: bond pdb=" N GLN C 298 " pdb=" CA GLN C 298 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.88e+00 bond pdb=" N GLN F 298 " pdb=" CA GLN F 298 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.87e+00 bond pdb=" N GLN D 298 " pdb=" CA GLN D 298 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.83e+00 bond pdb=" N GLN A 298 " pdb=" CA GLN A 298 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.27e-02 6.20e+03 5.70e+00 bond pdb=" N GLN B 298 " pdb=" CA GLN B 298 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.27e-02 6.20e+03 5.69e+00 ... (remaining 15409 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.79: 312 106.79 - 113.59: 8349 113.59 - 120.39: 6577 120.39 - 127.19: 5437 127.19 - 133.99: 103 Bond angle restraints: 20778 Sorted by residual: angle pdb=" N THR B 276 " pdb=" CA THR B 276 " pdb=" C THR B 276 " ideal model delta sigma weight residual 108.34 111.49 -3.15 1.31e+00 5.83e-01 5.78e+00 angle pdb=" N THR E 276 " pdb=" CA THR E 276 " pdb=" C THR E 276 " ideal model delta sigma weight residual 108.34 111.49 -3.15 1.31e+00 5.83e-01 5.77e+00 angle pdb=" N THR C 276 " pdb=" CA THR C 276 " pdb=" C THR C 276 " ideal model delta sigma weight residual 108.34 111.49 -3.15 1.31e+00 5.83e-01 5.77e+00 angle pdb=" N THR F 276 " pdb=" CA THR F 276 " pdb=" C THR F 276 " ideal model delta sigma weight residual 108.34 111.48 -3.14 1.31e+00 5.83e-01 5.73e+00 angle pdb=" N THR A 276 " pdb=" CA THR A 276 " pdb=" C THR A 276 " ideal model delta sigma weight residual 108.34 111.47 -3.13 1.31e+00 5.83e-01 5.70e+00 ... (remaining 20773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 8054 15.18 - 30.35: 1084 30.35 - 45.53: 294 45.53 - 60.70: 60 60.70 - 75.88: 36 Dihedral angle restraints: 9528 sinusoidal: 4002 harmonic: 5526 Sorted by residual: dihedral pdb=" CA GLU B 126 " pdb=" C GLU B 126 " pdb=" N GLY B 127 " pdb=" CA GLY B 127 " ideal model delta harmonic sigma weight residual -180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA GLU D 126 " pdb=" C GLU D 126 " pdb=" N GLY D 127 " pdb=" CA GLY D 127 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLU A 126 " pdb=" C GLU A 126 " pdb=" N GLY A 127 " pdb=" CA GLY A 127 " ideal model delta harmonic sigma weight residual 180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 9525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1267 0.027 - 0.054: 642 0.054 - 0.081: 193 0.081 - 0.109: 80 0.109 - 0.136: 26 Chirality restraints: 2208 Sorted by residual: chirality pdb=" CB ILE B 171 " pdb=" CA ILE B 171 " pdb=" CG1 ILE B 171 " pdb=" CG2 ILE B 171 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CB ILE D 171 " pdb=" CA ILE D 171 " pdb=" CG1 ILE D 171 " pdb=" CG2 ILE D 171 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CB ILE E 171 " pdb=" CA ILE E 171 " pdb=" CG1 ILE E 171 " pdb=" CG2 ILE E 171 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 2205 not shown) Planarity restraints: 2826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 346 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO C 347 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 347 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 347 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 346 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO E 347 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 347 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 346 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 347 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 347 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 347 " 0.025 5.00e-02 4.00e+02 ... (remaining 2823 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4750 2.82 - 3.34: 15895 3.34 - 3.86: 25778 3.86 - 4.38: 27270 4.38 - 4.90: 46431 Nonbonded interactions: 120124 Sorted by model distance: nonbonded pdb=" NE2 GLN B 191 " pdb=" OE1 GLN B 239 " model vdw 2.295 2.520 nonbonded pdb=" NE2 GLN D 191 " pdb=" OE1 GLN D 239 " model vdw 2.295 2.520 nonbonded pdb=" NE2 GLN E 191 " pdb=" OE1 GLN E 239 " model vdw 2.296 2.520 nonbonded pdb=" NE2 GLN A 191 " pdb=" OE1 GLN A 239 " model vdw 2.296 2.520 nonbonded pdb=" NE2 GLN C 191 " pdb=" OE1 GLN C 239 " model vdw 2.296 2.520 ... (remaining 120119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 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: 0.720 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: 3.820 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 42.940 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.090 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 : 0.004 0.033 15414 Z= 0.273 Angle : 0.562 4.755 20778 Z= 0.338 Chirality : 0.038 0.136 2208 Planarity : 0.003 0.046 2826 Dihedral : 15.540 75.878 5952 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.38 % Allowed : 8.27 % Favored : 91.35 % 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: -1.45 (0.18), residues: 1884 helix: -0.42 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -2.32 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.003 0.001 HIS C 182 PHE 0.009 0.001 PHE D 185 TYR 0.009 0.001 TYR A 163 ARG 0.009 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 433 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 437 average time/residue: 0.2912 time to fit residues: 182.6524 Evaluate side-chains 355 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 353 time to evaluate : 1.948 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1816 time to fit residues: 3.2873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 168 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN A 344 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 203 ASN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 344 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN E 203 ASN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN E 344 GLN ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN F 344 GLN ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15414 Z= 0.162 Angle : 0.519 9.796 20778 Z= 0.257 Chirality : 0.036 0.140 2208 Planarity : 0.004 0.041 2826 Dihedral : 3.739 16.096 2094 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.63 % Allowed : 15.85 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1884 helix: 0.78 (0.14), residues: 1434 sheet: None (None), residues: 0 loop : -1.60 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.001 0.001 HIS D 182 PHE 0.009 0.001 PHE E 185 TYR 0.012 0.001 TYR F 94 ARG 0.010 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 343 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 46 residues processed: 377 average time/residue: 0.2632 time to fit residues: 148.2691 Evaluate side-chains 367 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 321 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.1386 time to fit residues: 14.8059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 140 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 46 optimal weight: 0.0010 chunk 169 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15414 Z= 0.313 Angle : 0.561 8.076 20778 Z= 0.288 Chirality : 0.039 0.131 2208 Planarity : 0.004 0.040 2826 Dihedral : 3.855 16.847 2094 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.07 % Allowed : 20.86 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1884 helix: 1.14 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -1.73 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 366 HIS 0.003 0.002 HIS D 182 PHE 0.010 0.002 PHE F 185 TYR 0.013 0.002 TYR F 114 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 348 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 22 residues processed: 358 average time/residue: 0.2566 time to fit residues: 139.4117 Evaluate side-chains 343 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 321 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1370 time to fit residues: 8.2398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 179 optimal weight: 0.6980 chunk 88 optimal weight: 0.3980 chunk 160 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN E 314 ASN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15414 Z= 0.146 Angle : 0.484 6.251 20778 Z= 0.244 Chirality : 0.035 0.140 2208 Planarity : 0.003 0.037 2826 Dihedral : 3.471 15.141 2094 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.76 % Allowed : 21.93 % Favored : 75.31 % 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: 1.21 (0.20), residues: 1884 helix: 1.39 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -1.27 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 366 HIS 0.002 0.001 HIS D 182 PHE 0.009 0.001 PHE F 185 TYR 0.016 0.001 TYR A 94 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 332 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 31 residues processed: 354 average time/residue: 0.2642 time to fit residues: 141.1528 Evaluate side-chains 352 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 321 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1873 time to fit residues: 12.2467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15414 Z= 0.254 Angle : 0.513 6.790 20778 Z= 0.263 Chirality : 0.037 0.131 2208 Planarity : 0.003 0.038 2826 Dihedral : 3.604 16.258 2094 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.50 % Allowed : 24.12 % Favored : 74.37 % 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: 1.39 (0.20), residues: 1884 helix: 1.61 (0.14), residues: 1458 sheet: None (None), residues: 0 loop : -1.53 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 366 HIS 0.002 0.001 HIS B 182 PHE 0.010 0.001 PHE B 185 TYR 0.013 0.001 TYR A 94 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 329 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 20 residues processed: 336 average time/residue: 0.2571 time to fit residues: 131.0189 Evaluate side-chains 354 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 334 time to evaluate : 1.877 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1666 time to fit residues: 8.3462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 14 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 ASN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15414 Z= 0.152 Angle : 0.479 6.643 20778 Z= 0.243 Chirality : 0.035 0.136 2208 Planarity : 0.003 0.036 2826 Dihedral : 3.400 15.883 2094 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.50 % Allowed : 25.19 % Favored : 73.31 % 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: 1.60 (0.20), residues: 1884 helix: 1.70 (0.14), residues: 1482 sheet: None (None), residues: 0 loop : -1.34 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 366 HIS 0.001 0.001 HIS E 182 PHE 0.009 0.001 PHE E 185 TYR 0.015 0.001 TYR A 94 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 338 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 19 residues processed: 347 average time/residue: 0.2613 time to fit residues: 137.3016 Evaluate side-chains 343 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 324 time to evaluate : 1.916 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1581 time to fit residues: 8.0092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15414 Z= 0.239 Angle : 0.522 7.126 20778 Z= 0.268 Chirality : 0.037 0.133 2208 Planarity : 0.003 0.038 2826 Dihedral : 3.541 16.767 2094 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.57 % Allowed : 26.38 % Favored : 72.06 % 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: 1.66 (0.20), residues: 1884 helix: 1.75 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -1.30 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 366 HIS 0.002 0.001 HIS E 182 PHE 0.021 0.001 PHE F 129 TYR 0.013 0.001 TYR A 94 ARG 0.008 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 329 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 339 average time/residue: 0.2504 time to fit residues: 129.1840 Evaluate side-chains 337 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 320 time to evaluate : 1.727 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1288 time to fit residues: 6.5758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 122 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15414 Z= 0.179 Angle : 0.510 7.263 20778 Z= 0.261 Chirality : 0.036 0.184 2208 Planarity : 0.003 0.034 2826 Dihedral : 3.486 17.603 2094 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.88 % Allowed : 27.01 % Favored : 72.12 % 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: 1.77 (0.20), residues: 1884 helix: 1.83 (0.14), residues: 1482 sheet: None (None), residues: 0 loop : -1.30 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 366 HIS 0.002 0.001 HIS E 182 PHE 0.023 0.001 PHE F 129 TYR 0.015 0.001 TYR A 94 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 325 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 326 average time/residue: 0.2560 time to fit residues: 125.9331 Evaluate side-chains 331 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 318 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1334 time to fit residues: 5.7716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 chunk 158 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15414 Z= 0.169 Angle : 0.528 10.151 20778 Z= 0.267 Chirality : 0.036 0.131 2208 Planarity : 0.003 0.033 2826 Dihedral : 3.476 19.566 2094 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.56 % Allowed : 28.76 % Favored : 70.68 % 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: 1.82 (0.20), residues: 1884 helix: 1.88 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -1.32 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 287 HIS 0.002 0.001 HIS D 182 PHE 0.024 0.001 PHE F 129 TYR 0.017 0.001 TYR A 94 ARG 0.005 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 306 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 309 average time/residue: 0.2542 time to fit residues: 119.2557 Evaluate side-chains 305 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 301 time to evaluate : 1.930 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1430 time to fit residues: 3.7161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 185 optimal weight: 5.9990 chunk 170 optimal weight: 0.0170 chunk 147 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 113 optimal weight: 0.7980 chunk 90 optimal weight: 0.0050 overall best weight: 0.2632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15414 Z= 0.140 Angle : 0.537 11.413 20778 Z= 0.266 Chirality : 0.034 0.131 2208 Planarity : 0.003 0.036 2826 Dihedral : 3.369 17.810 2094 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.31 % Allowed : 29.95 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.20), residues: 1884 helix: 2.14 (0.14), residues: 1446 sheet: None (None), residues: 0 loop : -1.24 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 287 HIS 0.001 0.000 HIS D 140 PHE 0.021 0.001 PHE F 129 TYR 0.018 0.001 TYR A 94 ARG 0.004 0.000 ARG E 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 304 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 306 average time/residue: 0.2632 time to fit residues: 122.0828 Evaluate side-chains 288 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 287 time to evaluate : 1.919 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4594 time to fit residues: 3.2027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 298 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 288 ASN ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.103423 restraints weight = 25030.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106876 restraints weight = 13499.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109071 restraints weight = 8430.018| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15414 Z= 0.174 Angle : 0.540 11.050 20778 Z= 0.272 Chirality : 0.036 0.136 2208 Planarity : 0.003 0.042 2826 Dihedral : 3.422 17.883 2094 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.88 % Allowed : 30.08 % Favored : 69.05 % 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: 1.97 (0.20), residues: 1884 helix: 2.09 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : -1.84 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 366 HIS 0.002 0.001 HIS D 182 PHE 0.026 0.001 PHE F 129 TYR 0.018 0.001 TYR A 94 ARG 0.007 0.000 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3176.24 seconds wall clock time: 58 minutes 35.72 seconds (3515.72 seconds total)