Starting phenix.real_space_refine on Thu Feb 15 17:00:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osg_13050/02_2024/7osg_13050.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osg_13050/02_2024/7osg_13050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osg_13050/02_2024/7osg_13050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osg_13050/02_2024/7osg_13050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osg_13050/02_2024/7osg_13050.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osg_13050/02_2024/7osg_13050.pdb" } resolution = 3.3 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 Mg 1 5.21 5 S 45 5.16 5 C 8203 2.51 5 N 2250 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 292": "NH1" <-> "NH2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H ARG 152": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12831 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3077 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2375 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain: "C" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2015 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Chain: "E" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1896 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Chain: "H" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1097 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 138} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11844 SG CYS H 45 45.534 43.242 48.186 1.00110.24 S ATOM 11867 SG CYS H 48 43.342 44.334 45.851 1.00107.87 S ATOM 12048 SG CYS H 72 46.293 45.139 44.175 1.00111.38 S Time building chain proxies: 7.33, per 1000 atoms: 0.57 Number of scatterers: 12831 At special positions: 0 Unit cell: (80.352, 92.016, 190.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 S 45 16.00 Mg 1 11.99 O 2330 8.00 N 2250 7.00 C 8203 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: 5.11 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 45 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 48 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 72 " 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2998 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 13 sheets defined 46.6% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 344 through 348 removed outlier: 4.287A pdb=" N GLY A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.649A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.530A pdb=" N MET A 390 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.623A pdb=" N TRP A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.602A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.649A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 4.184A pdb=" N VAL B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 192' Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 232 through 243 removed outlier: 4.200A pdb=" N GLN B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ARG B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 removed outlier: 3.532A pdb=" N LEU B 267 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.517A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 50 " --> pdb=" O MET C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 106 through 111 removed outlier: 4.432A pdb=" N ASP C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 106 through 111' Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 177 removed outlier: 3.713A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 192 removed outlier: 4.070A pdb=" N VAL C 191 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 192' Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 240 through 244 removed outlier: 3.735A pdb=" N ALA C 243 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 removed outlier: 3.680A pdb=" N LEU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.010A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.534A pdb=" N PHE D 28 " --> pdb=" O ILE D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.620A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Proline residue: D 67 - end of helix Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.679A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.179A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 167 removed outlier: 3.532A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.667A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.570A pdb=" N SER D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 216 through 226 Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.701A pdb=" N LEU D 239 " --> pdb=" O MET D 236 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER D 240 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.621A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.688A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.562A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.528A pdb=" N ALA E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 85 through 92 removed outlier: 3.608A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR E 92 " --> pdb=" O MET E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.636A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 135 through 143 removed outlier: 3.808A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.575A pdb=" N VAL E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.565A pdb=" N ALA E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.658A pdb=" N LEU E 196 " --> pdb=" O VAL E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 removed outlier: 4.047A pdb=" N TRP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.511A pdb=" N ILE E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 272 removed outlier: 4.105A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 55 removed outlier: 3.773A pdb=" N ASP H 54 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 82 Processing helix chain 'H' and resid 113 through 117 removed outlier: 3.523A pdb=" N SER H 116 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 113 through 117' Processing helix chain 'H' and resid 139 through 150 removed outlier: 3.683A pdb=" N GLY H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 172 removed outlier: 3.689A pdb=" N GLN H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47 removed outlier: 6.193A pdb=" N TRP A 45 " --> pdb=" O ARG A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.759A pdb=" N GLN A 73 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.368A pdb=" N PHE A 56 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY A 131 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 333 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N HIS A 311 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.646A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL A 142 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217 removed outlier: 7.725A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 298 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 25 removed outlier: 5.853A pdb=" N VAL B 9 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN B 23 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN B 7 " --> pdb=" O ASN B 23 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN B 25 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU B 5 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.528A pdb=" N GLY B 77 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ASP B 153 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 31 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA B 199 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 201 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE B 35 " --> pdb=" O LEU B 201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 248 removed outlier: 4.020A pdb=" N GLU B 256 " --> pdb=" O ARG B 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.312A pdb=" N GLY C 77 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASP C 153 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 79 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA C 202 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 249 removed outlier: 4.083A pdb=" N ARG C 248 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA C 227 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 228 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 279 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AB4, first strand: chain 'H' and resid 119 through 120 525 hydrogen bonds defined for protein. 1473 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: 3.66 Time building geometry restraints manager: 5.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4177 1.34 - 1.46: 2805 1.46 - 1.58: 6011 1.58 - 1.70: 2 1.70 - 1.83: 77 Bond restraints: 13072 Sorted by residual: bond pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 1.525 1.583 -0.058 2.10e-02 2.27e+03 7.75e+00 bond pdb=" CB VAL A 336 " pdb=" CG1 VAL A 336 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.89e+00 bond pdb=" CB GLN A 232 " pdb=" CG GLN A 232 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.17e+00 bond pdb=" CG1 ILE B 195 " pdb=" CD1 ILE B 195 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.84e+00 bond pdb=" C LEU E 209 " pdb=" N PRO E 210 " ideal model delta sigma weight residual 1.335 1.362 -0.026 1.36e-02 5.41e+03 3.72e+00 ... (remaining 13067 not shown) Histogram of bond angle deviations from ideal: 91.72 - 100.28: 13 100.28 - 108.83: 1024 108.83 - 117.38: 8332 117.38 - 125.93: 8099 125.93 - 134.49: 265 Bond angle restraints: 17733 Sorted by residual: angle pdb=" CA HIS C 37 " pdb=" C HIS C 37 " pdb=" N ASN C 38 " ideal model delta sigma weight residual 119.46 116.46 3.00 6.10e-01 2.69e+00 2.43e+01 angle pdb=" CB MET B 295 " pdb=" CG MET B 295 " pdb=" SD MET B 295 " ideal model delta sigma weight residual 112.70 126.72 -14.02 3.00e+00 1.11e-01 2.18e+01 angle pdb=" C GLU H 64 " pdb=" N LYS H 65 " pdb=" CA LYS H 65 " ideal model delta sigma weight residual 125.02 133.17 -8.15 1.76e+00 3.23e-01 2.15e+01 angle pdb=" N GLY B 299 " pdb=" CA GLY B 299 " pdb=" C GLY B 299 " ideal model delta sigma weight residual 113.48 120.15 -6.67 1.46e+00 4.69e-01 2.09e+01 angle pdb=" CA LEU A 35 " pdb=" CB LEU A 35 " pdb=" CG LEU A 35 " ideal model delta sigma weight residual 116.30 132.23 -15.93 3.50e+00 8.16e-02 2.07e+01 ... (remaining 17728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 6883 17.72 - 35.45: 695 35.45 - 53.17: 132 53.17 - 70.90: 25 70.90 - 88.62: 4 Dihedral angle restraints: 7739 sinusoidal: 3041 harmonic: 4698 Sorted by residual: dihedral pdb=" CA GLU B 305 " pdb=" C GLU B 305 " pdb=" N GLY B 306 " pdb=" CA GLY B 306 " ideal model delta harmonic sigma weight residual 180.00 148.24 31.76 0 5.00e+00 4.00e-02 4.04e+01 dihedral pdb=" CA ASP H 108 " pdb=" C ASP H 108 " pdb=" N GLY H 109 " pdb=" CA GLY H 109 " ideal model delta harmonic sigma weight residual 180.00 148.74 31.26 0 5.00e+00 4.00e-02 3.91e+01 dihedral pdb=" CA ARG C 307 " pdb=" C ARG C 307 " pdb=" N LEU C 308 " pdb=" CA LEU C 308 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 7736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1723 0.081 - 0.162: 266 0.162 - 0.244: 36 0.244 - 0.325: 5 0.325 - 0.406: 1 Chirality restraints: 2031 Sorted by residual: chirality pdb=" CB VAL A 413 " pdb=" CA VAL A 413 " pdb=" CG1 VAL A 413 " pdb=" CG2 VAL A 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA ASP A 182 " pdb=" N ASP A 182 " pdb=" C ASP A 182 " pdb=" CB ASP A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU E 199 " pdb=" CB LEU E 199 " pdb=" CD1 LEU E 199 " pdb=" CD2 LEU E 199 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 2028 not shown) Planarity restraints: 2277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 209 " -0.068 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO E 210 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 43 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C THR C 43 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 43 " -0.020 2.00e-02 2.50e+03 pdb=" N THR C 44 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " 0.050 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO D 67 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.042 5.00e-02 4.00e+02 ... (remaining 2274 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 100 2.55 - 3.14: 9104 3.14 - 3.72: 20067 3.72 - 4.31: 28451 4.31 - 4.90: 47202 Nonbonded interactions: 104924 Sorted by model distance: nonbonded pdb=" OE1 GLU H 76 " pdb="ZN ZN H 201 " model vdw 1.962 2.230 nonbonded pdb=" NE2 HIS A 207 " pdb="CU CU A 502 " model vdw 2.069 2.320 nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 2.086 2.170 nonbonded pdb=" OD1 ASP A 359 " pdb="MG MG A 501 " model vdw 2.091 2.170 nonbonded pdb=" OD1 ASP A 367 " pdb="MG MG A 501 " model vdw 2.129 2.170 ... (remaining 104919 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 'B' and resid 2 through 308) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through \ 274)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 2.490 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 39.160 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 0.080 13072 Z= 0.531 Angle : 1.075 15.927 17733 Z= 0.570 Chirality : 0.062 0.406 2031 Planarity : 0.007 0.101 2277 Dihedral : 14.454 88.625 4741 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.97 % Allowed : 9.23 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.46 (0.15), residues: 1646 helix: -4.31 (0.09), residues: 699 sheet: -3.23 (0.29), residues: 210 loop : -2.86 (0.19), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 240 HIS 0.024 0.002 HIS C 37 PHE 0.034 0.002 PHE B 35 TYR 0.028 0.002 TYR C 291 ARG 0.006 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.9331 (mmtt) cc_final: 0.9101 (tppp) REVERT: B 57 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: B 61 LYS cc_start: 0.8461 (mttp) cc_final: 0.8110 (mmmm) REVERT: B 84 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8668 (p) REVERT: B 283 HIS cc_start: 0.9114 (m90) cc_final: 0.8774 (m90) REVERT: D 66 MET cc_start: 0.8869 (mmm) cc_final: 0.8660 (mmt) REVERT: D 82 ASP cc_start: 0.8786 (t70) cc_final: 0.8450 (t0) REVERT: D 190 ASP cc_start: 0.8584 (m-30) cc_final: 0.8272 (m-30) REVERT: E 82 ASP cc_start: 0.9040 (t0) cc_final: 0.8635 (t0) REVERT: H 40 HIS cc_start: 0.8650 (m-70) cc_final: 0.8198 (m-70) REVERT: H 43 ASP cc_start: 0.7819 (m-30) cc_final: 0.7336 (m-30) REVERT: H 65 LYS cc_start: 0.8710 (pttm) cc_final: 0.8473 (pttm) REVERT: H 92 LYS cc_start: 0.8949 (tttp) cc_final: 0.8731 (mtpp) REVERT: H 104 GLU cc_start: 0.8820 (mp0) cc_final: 0.8541 (mp0) REVERT: H 141 ASP cc_start: 0.8496 (p0) cc_final: 0.8100 (p0) REVERT: H 143 LYS cc_start: 0.9312 (mmtt) cc_final: 0.8955 (mmtm) REVERT: H 157 GLU cc_start: 0.8375 (pp20) cc_final: 0.8048 (pp20) REVERT: H 158 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7772 (mt-10) REVERT: H 165 GLN cc_start: 0.8443 (mt0) cc_final: 0.8161 (mt0) REVERT: H 166 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8162 (tp30) REVERT: H 170 MET cc_start: 0.8460 (mmp) cc_final: 0.7604 (mmm) outliers start: 13 outliers final: 4 residues processed: 158 average time/residue: 0.3403 time to fit residues: 71.8182 Evaluate side-chains 99 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 250 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 66 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 0.2980 chunk 95 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 77 GLN A 123 ASN A 141 GLN A 145 ASN A 174 HIS A 175 ASN A 179 ASN A 190 ASN A 212 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 324 ASN B 20 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 270 GLN C 25 ASN C 115 GLN C 194 HIS D 225 ASN E 108 HIS E 225 ASN H 149 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13072 Z= 0.148 Angle : 0.565 7.400 17733 Z= 0.293 Chirality : 0.041 0.201 2031 Planarity : 0.005 0.058 2277 Dihedral : 5.486 51.351 1813 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.56 % Allowed : 13.18 % Favored : 85.26 % 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: -3.35 (0.18), residues: 1646 helix: -1.77 (0.16), residues: 715 sheet: -2.79 (0.31), residues: 220 loop : -2.38 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 211 HIS 0.003 0.001 HIS C 37 PHE 0.010 0.001 PHE A 289 TYR 0.019 0.001 TYR C 13 ARG 0.004 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.9237 (mmtt) cc_final: 0.9012 (ttmm) REVERT: A 305 LYS cc_start: 0.8978 (mtmm) cc_final: 0.8663 (mtmt) REVERT: B 61 LYS cc_start: 0.8286 (mttp) cc_final: 0.8055 (mmmm) REVERT: B 283 HIS cc_start: 0.9121 (m90) cc_final: 0.8807 (m90) REVERT: D 82 ASP cc_start: 0.8700 (t70) cc_final: 0.8428 (t0) REVERT: D 88 MET cc_start: 0.8307 (tpp) cc_final: 0.8092 (tpp) REVERT: D 135 GLU cc_start: 0.7928 (tp30) cc_final: 0.7717 (pm20) REVERT: D 190 ASP cc_start: 0.8498 (m-30) cc_final: 0.8266 (m-30) REVERT: D 230 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7417 (tm-30) REVERT: E 82 ASP cc_start: 0.8904 (t0) cc_final: 0.8485 (t0) REVERT: H 40 HIS cc_start: 0.8535 (m-70) cc_final: 0.8072 (m-70) REVERT: H 43 ASP cc_start: 0.7589 (m-30) cc_final: 0.7084 (m-30) REVERT: H 143 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8700 (mmtm) outliers start: 21 outliers final: 10 residues processed: 127 average time/residue: 0.3471 time to fit residues: 61.4161 Evaluate side-chains 100 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 54 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 147 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 238 GLN C 283 HIS E 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13072 Z= 0.271 Angle : 0.591 8.340 17733 Z= 0.297 Chirality : 0.042 0.172 2031 Planarity : 0.004 0.045 2277 Dihedral : 4.856 34.565 1808 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.31 % Allowed : 15.19 % Favored : 82.50 % 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: -1.94 (0.20), residues: 1646 helix: -0.07 (0.19), residues: 718 sheet: -2.49 (0.32), residues: 221 loop : -2.12 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 20 HIS 0.003 0.001 HIS A 174 PHE 0.017 0.001 PHE D 157 TYR 0.018 0.001 TYR C 13 ARG 0.005 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9677 (OUTLIER) cc_final: 0.9468 (mp) REVERT: A 235 LYS cc_start: 0.9291 (mmtt) cc_final: 0.9044 (ttmm) REVERT: A 305 LYS cc_start: 0.9080 (mtmm) cc_final: 0.8773 (mtmt) REVERT: B 16 MET cc_start: 0.8789 (pmm) cc_final: 0.8519 (pmm) REVERT: B 57 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6619 (tm-30) REVERT: B 61 LYS cc_start: 0.8342 (mttp) cc_final: 0.8110 (mmmm) REVERT: B 133 MET cc_start: 0.8947 (mtp) cc_final: 0.8598 (mtm) REVERT: C 110 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7910 (p0) REVERT: C 295 MET cc_start: 0.8986 (mmm) cc_final: 0.8718 (mmm) REVERT: D 66 MET cc_start: 0.8399 (mmm) cc_final: 0.8177 (mmm) REVERT: D 82 ASP cc_start: 0.8761 (t70) cc_final: 0.8430 (t0) REVERT: D 88 MET cc_start: 0.8216 (tpp) cc_final: 0.7839 (tpp) REVERT: E 10 LYS cc_start: 0.9036 (tmtt) cc_final: 0.8518 (tmtt) REVERT: E 11 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7938 (mm-30) REVERT: E 66 MET cc_start: 0.8697 (mmp) cc_final: 0.8372 (tpp) REVERT: E 81 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7925 (mm-30) REVERT: E 82 ASP cc_start: 0.8931 (t0) cc_final: 0.8545 (t0) REVERT: E 138 MET cc_start: 0.8456 (tmm) cc_final: 0.8076 (tmm) REVERT: H 40 HIS cc_start: 0.8540 (m-70) cc_final: 0.8265 (m170) REVERT: H 65 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8258 (ptpp) REVERT: H 143 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8720 (mmtm) outliers start: 31 outliers final: 18 residues processed: 124 average time/residue: 0.2755 time to fit residues: 49.1109 Evaluate side-chains 106 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 chunk 148 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 283 HIS E 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13072 Z= 0.202 Angle : 0.540 9.322 17733 Z= 0.271 Chirality : 0.041 0.155 2031 Planarity : 0.003 0.042 2277 Dihedral : 4.662 33.238 1808 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.68 % Allowed : 16.68 % Favored : 80.64 % 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: -1.29 (0.21), residues: 1646 helix: 0.77 (0.21), residues: 717 sheet: -2.53 (0.31), residues: 243 loop : -1.97 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 20 HIS 0.003 0.001 HIS B 37 PHE 0.013 0.001 PHE D 157 TYR 0.009 0.001 TYR B 86 ARG 0.007 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9668 (OUTLIER) cc_final: 0.9462 (mp) REVERT: A 235 LYS cc_start: 0.9229 (mmtt) cc_final: 0.9027 (ttmm) REVERT: A 305 LYS cc_start: 0.9062 (mtmm) cc_final: 0.8741 (mtmt) REVERT: B 16 MET cc_start: 0.8768 (pmm) cc_final: 0.8376 (pmm) REVERT: B 57 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: B 61 LYS cc_start: 0.8387 (mttp) cc_final: 0.8149 (mmmm) REVERT: B 183 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8501 (mt) REVERT: C 295 MET cc_start: 0.8833 (mmm) cc_final: 0.8617 (mmm) REVERT: D 66 MET cc_start: 0.8511 (mmm) cc_final: 0.8252 (mmm) REVERT: D 82 ASP cc_start: 0.8771 (t70) cc_final: 0.8443 (t0) REVERT: D 88 MET cc_start: 0.8251 (tpp) cc_final: 0.7826 (tpp) REVERT: E 10 LYS cc_start: 0.9057 (tmtt) cc_final: 0.8838 (tmtt) REVERT: E 66 MET cc_start: 0.8707 (mmp) cc_final: 0.8407 (tpp) REVERT: E 82 ASP cc_start: 0.8955 (t0) cc_final: 0.8546 (t0) REVERT: E 138 MET cc_start: 0.8467 (tmm) cc_final: 0.8098 (tmm) REVERT: H 40 HIS cc_start: 0.8404 (m-70) cc_final: 0.8089 (m-70) REVERT: H 65 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8113 (ptpp) REVERT: H 94 TYR cc_start: 0.8782 (m-80) cc_final: 0.8279 (m-10) REVERT: H 143 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8707 (mmtm) outliers start: 36 outliers final: 20 residues processed: 123 average time/residue: 0.2754 time to fit residues: 48.7400 Evaluate side-chains 110 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN B 11 GLN B 37 HIS ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13072 Z= 0.298 Angle : 0.583 8.463 17733 Z= 0.290 Chirality : 0.042 0.148 2031 Planarity : 0.003 0.037 2277 Dihedral : 4.693 34.452 1808 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.76 % Allowed : 16.75 % Favored : 80.49 % 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: -0.88 (0.22), residues: 1646 helix: 1.25 (0.21), residues: 716 sheet: -2.40 (0.30), residues: 255 loop : -1.86 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 20 HIS 0.004 0.001 HIS A 174 PHE 0.017 0.001 PHE D 157 TYR 0.009 0.001 TYR A 258 ARG 0.007 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 87 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9668 (OUTLIER) cc_final: 0.9465 (mp) REVERT: A 235 LYS cc_start: 0.9258 (mmtt) cc_final: 0.9049 (ttmm) REVERT: A 305 LYS cc_start: 0.9095 (mtmm) cc_final: 0.8734 (mtmt) REVERT: B 16 MET cc_start: 0.8761 (pmm) cc_final: 0.8418 (pmm) REVERT: B 57 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6619 (tm-30) REVERT: B 61 LYS cc_start: 0.8336 (mttp) cc_final: 0.8109 (mmmm) REVERT: B 183 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8204 (mm) REVERT: C 295 MET cc_start: 0.8827 (mmm) cc_final: 0.8626 (mmm) REVERT: D 66 MET cc_start: 0.8602 (mmm) cc_final: 0.8337 (mmm) REVERT: D 82 ASP cc_start: 0.8805 (t70) cc_final: 0.8475 (t0) REVERT: D 88 MET cc_start: 0.8275 (tpp) cc_final: 0.7927 (tpp) REVERT: E 81 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7983 (mm-30) REVERT: E 82 ASP cc_start: 0.9005 (t0) cc_final: 0.8595 (t0) REVERT: E 138 MET cc_start: 0.8285 (tmm) cc_final: 0.7931 (tmm) REVERT: H 40 HIS cc_start: 0.8372 (m-70) cc_final: 0.8087 (m-70) REVERT: H 65 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8152 (ptpp) REVERT: H 143 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8722 (mmtm) outliers start: 37 outliers final: 25 residues processed: 119 average time/residue: 0.2537 time to fit residues: 44.3540 Evaluate side-chains 112 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 83 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 73 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN B 37 HIS ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13072 Z= 0.139 Angle : 0.505 10.150 17733 Z= 0.253 Chirality : 0.040 0.138 2031 Planarity : 0.003 0.036 2277 Dihedral : 4.398 31.483 1808 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.76 % Allowed : 17.50 % Favored : 79.75 % 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: -0.48 (0.22), residues: 1646 helix: 1.63 (0.21), residues: 716 sheet: -2.03 (0.30), residues: 269 loop : -1.77 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 98 HIS 0.003 0.001 HIS B 20 PHE 0.010 0.001 PHE D 157 TYR 0.009 0.001 TYR E 221 ARG 0.008 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 93 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9092 (mtmm) cc_final: 0.8746 (mtmt) REVERT: B 57 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6393 (tm-30) REVERT: B 61 LYS cc_start: 0.8426 (mttp) cc_final: 0.8197 (mmmm) REVERT: B 86 TYR cc_start: 0.9151 (m-80) cc_final: 0.8944 (m-80) REVERT: B 183 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8025 (mm) REVERT: D 66 MET cc_start: 0.8489 (mmm) cc_final: 0.8222 (mmm) REVERT: D 82 ASP cc_start: 0.8754 (t70) cc_final: 0.8456 (t0) REVERT: D 88 MET cc_start: 0.8248 (tpp) cc_final: 0.7877 (tpp) REVERT: E 10 LYS cc_start: 0.9001 (tmtt) cc_final: 0.8324 (tmtt) REVERT: E 66 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8345 (tpp) REVERT: E 81 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7735 (mm-30) REVERT: E 82 ASP cc_start: 0.8977 (t0) cc_final: 0.8562 (t0) REVERT: E 138 MET cc_start: 0.8303 (tmm) cc_final: 0.7918 (tmm) REVERT: H 40 HIS cc_start: 0.8439 (m-70) cc_final: 0.8109 (m-70) REVERT: H 65 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8085 (ptpp) REVERT: H 143 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8675 (mmtm) outliers start: 37 outliers final: 21 residues processed: 125 average time/residue: 0.2582 time to fit residues: 47.5261 Evaluate side-chains 109 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13072 Z= 0.401 Angle : 0.643 10.664 17733 Z= 0.317 Chirality : 0.044 0.147 2031 Planarity : 0.003 0.034 2277 Dihedral : 4.668 35.817 1806 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.98 % Allowed : 17.87 % Favored : 79.15 % 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: -0.52 (0.22), residues: 1646 helix: 1.58 (0.21), residues: 720 sheet: -2.35 (0.30), residues: 254 loop : -1.67 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 20 HIS 0.006 0.001 HIS B 37 PHE 0.020 0.002 PHE D 157 TYR 0.013 0.002 TYR H 94 ARG 0.008 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 80 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9660 (OUTLIER) cc_final: 0.9438 (mp) REVERT: A 305 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8738 (mtmt) REVERT: B 57 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6624 (tm-30) REVERT: B 61 LYS cc_start: 0.8363 (mttp) cc_final: 0.8130 (mmmm) REVERT: B 82 ASN cc_start: 0.9139 (p0) cc_final: 0.8889 (p0) REVERT: B 133 MET cc_start: 0.9039 (mtp) cc_final: 0.8604 (mtm) REVERT: B 183 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8252 (mm) REVERT: D 82 ASP cc_start: 0.8832 (t70) cc_final: 0.8495 (t0) REVERT: D 88 MET cc_start: 0.8308 (tpp) cc_final: 0.7936 (tpp) REVERT: E 10 LYS cc_start: 0.8859 (tmtt) cc_final: 0.8411 (tmtt) REVERT: E 81 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7990 (mm-30) REVERT: E 82 ASP cc_start: 0.9032 (t0) cc_final: 0.8629 (t0) REVERT: E 138 MET cc_start: 0.8296 (tmm) cc_final: 0.7926 (tmm) REVERT: H 40 HIS cc_start: 0.8395 (m-70) cc_final: 0.8078 (m-70) REVERT: H 65 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8096 (ptpp) REVERT: H 94 TYR cc_start: 0.8825 (m-10) cc_final: 0.8577 (m-10) REVERT: H 143 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8739 (mmtm) outliers start: 40 outliers final: 28 residues processed: 112 average time/residue: 0.2572 time to fit residues: 42.8073 Evaluate side-chains 109 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 77 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS B 37 HIS ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13072 Z= 0.192 Angle : 0.550 10.700 17733 Z= 0.271 Chirality : 0.041 0.148 2031 Planarity : 0.003 0.033 2277 Dihedral : 4.478 33.709 1806 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.31 % Allowed : 18.69 % Favored : 79.00 % 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: -0.37 (0.22), residues: 1646 helix: 1.75 (0.21), residues: 718 sheet: -2.28 (0.31), residues: 244 loop : -1.65 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 20 HIS 0.004 0.001 HIS A 417 PHE 0.013 0.001 PHE D 157 TYR 0.010 0.001 TYR B 291 ARG 0.008 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 87 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9120 (mtmm) cc_final: 0.8761 (mtmt) REVERT: B 57 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6524 (tm-30) REVERT: B 61 LYS cc_start: 0.8438 (mttp) cc_final: 0.8204 (mmmm) REVERT: B 133 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8159 (mtp) REVERT: B 183 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8166 (mm) REVERT: D 82 ASP cc_start: 0.8787 (t70) cc_final: 0.8472 (t0) REVERT: D 88 MET cc_start: 0.8285 (tpp) cc_final: 0.7903 (tpp) REVERT: D 190 ASP cc_start: 0.8354 (m-30) cc_final: 0.8085 (m-30) REVERT: E 81 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7899 (mm-30) REVERT: E 82 ASP cc_start: 0.9010 (t0) cc_final: 0.8594 (t0) REVERT: E 138 MET cc_start: 0.8296 (tmm) cc_final: 0.7991 (tmm) REVERT: H 40 HIS cc_start: 0.8419 (m-70) cc_final: 0.8066 (m-70) REVERT: H 65 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8054 (ptpp) REVERT: H 94 TYR cc_start: 0.8793 (m-10) cc_final: 0.8553 (m-10) REVERT: H 143 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8700 (mmtm) outliers start: 31 outliers final: 23 residues processed: 112 average time/residue: 0.2603 time to fit residues: 42.9593 Evaluate side-chains 108 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 81 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS B 37 HIS ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13072 Z= 0.220 Angle : 0.557 11.455 17733 Z= 0.273 Chirality : 0.042 0.185 2031 Planarity : 0.003 0.035 2277 Dihedral : 4.431 33.934 1806 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.23 % Allowed : 18.84 % Favored : 78.93 % 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: -0.31 (0.22), residues: 1646 helix: 1.79 (0.21), residues: 719 sheet: -2.24 (0.31), residues: 244 loop : -1.62 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 20 HIS 0.003 0.001 HIS B 245 PHE 0.014 0.001 PHE D 157 TYR 0.018 0.001 TYR B 86 ARG 0.008 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9670 (OUTLIER) cc_final: 0.9448 (mp) REVERT: A 62 MET cc_start: 0.7781 (mmp) cc_final: 0.7132 (mmp) REVERT: A 305 LYS cc_start: 0.9114 (mtmm) cc_final: 0.8754 (mtmt) REVERT: B 57 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6458 (tm-30) REVERT: B 61 LYS cc_start: 0.8439 (mttp) cc_final: 0.8207 (mmmm) REVERT: B 133 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8637 (mtm) REVERT: B 183 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8384 (mm) REVERT: C 133 MET cc_start: 0.8694 (mtm) cc_final: 0.8299 (mtm) REVERT: D 82 ASP cc_start: 0.8805 (t70) cc_final: 0.8495 (t0) REVERT: D 88 MET cc_start: 0.8318 (tpp) cc_final: 0.7948 (tpp) REVERT: D 190 ASP cc_start: 0.8361 (m-30) cc_final: 0.8086 (m-30) REVERT: E 66 MET cc_start: 0.8684 (mmp) cc_final: 0.8303 (tpp) REVERT: E 81 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7972 (mm-30) REVERT: E 82 ASP cc_start: 0.9016 (t0) cc_final: 0.8610 (t0) REVERT: E 138 MET cc_start: 0.8301 (tmm) cc_final: 0.8012 (tmm) REVERT: H 40 HIS cc_start: 0.8415 (m-70) cc_final: 0.8069 (m-70) REVERT: H 65 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8058 (ptpp) REVERT: H 94 TYR cc_start: 0.8793 (m-10) cc_final: 0.8546 (m-10) REVERT: H 143 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8702 (mmtm) outliers start: 30 outliers final: 24 residues processed: 110 average time/residue: 0.2669 time to fit residues: 43.3568 Evaluate side-chains 109 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 80 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 149 optimal weight: 0.0970 chunk 129 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 99 optimal weight: 0.0070 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS B 37 HIS H 96 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13072 Z= 0.149 Angle : 0.533 11.727 17733 Z= 0.262 Chirality : 0.041 0.159 2031 Planarity : 0.003 0.035 2277 Dihedral : 4.281 32.025 1806 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.31 % Allowed : 18.91 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1646 helix: 1.92 (0.21), residues: 719 sheet: -1.80 (0.31), residues: 269 loop : -1.62 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 98 HIS 0.008 0.001 HIS A 417 PHE 0.011 0.001 PHE D 157 TYR 0.014 0.001 TYR B 86 ARG 0.009 0.000 ARG H 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 87 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9438 (mp) REVERT: A 305 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8761 (mtmt) REVERT: A 390 MET cc_start: 0.8371 (mmm) cc_final: 0.7934 (tpp) REVERT: B 57 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6775 (tm-30) REVERT: B 61 LYS cc_start: 0.8448 (mttp) cc_final: 0.8215 (mmmm) REVERT: B 133 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8589 (mtm) REVERT: B 183 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8388 (mm) REVERT: C 42 LYS cc_start: 0.8816 (tttm) cc_final: 0.8473 (tttm) REVERT: D 82 ASP cc_start: 0.8764 (t70) cc_final: 0.8475 (t0) REVERT: D 88 MET cc_start: 0.8305 (tpp) cc_final: 0.7912 (tpp) REVERT: D 190 ASP cc_start: 0.8344 (m-30) cc_final: 0.8104 (m-30) REVERT: E 66 MET cc_start: 0.8606 (mmp) cc_final: 0.8286 (tpp) REVERT: E 81 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7905 (mm-30) REVERT: E 82 ASP cc_start: 0.8999 (t0) cc_final: 0.8586 (t0) REVERT: E 138 MET cc_start: 0.8304 (tmm) cc_final: 0.8043 (tmm) REVERT: H 40 HIS cc_start: 0.8389 (m-70) cc_final: 0.8066 (m-70) REVERT: H 65 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8062 (ptpp) REVERT: H 94 TYR cc_start: 0.8760 (m-10) cc_final: 0.8510 (m-10) REVERT: H 143 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8675 (mmtm) outliers start: 31 outliers final: 24 residues processed: 113 average time/residue: 0.2601 time to fit residues: 43.3982 Evaluate side-chains 112 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 83 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 141 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 129 optimal weight: 0.4980 chunk 54 optimal weight: 0.4980 chunk 132 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS B 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.070919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052306 restraints weight = 39744.768| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.58 r_work: 0.2818 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13072 Z= 0.142 Angle : 0.527 11.966 17733 Z= 0.258 Chirality : 0.040 0.149 2031 Planarity : 0.003 0.046 2277 Dihedral : 4.202 31.788 1806 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.23 % Allowed : 19.14 % Favored : 78.63 % 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: -0.05 (0.22), residues: 1646 helix: 1.99 (0.21), residues: 720 sheet: -1.86 (0.31), residues: 278 loop : -1.54 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 98 HIS 0.007 0.001 HIS A 417 PHE 0.011 0.001 PHE D 157 TYR 0.012 0.001 TYR B 86 ARG 0.011 0.000 ARG H 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2550.47 seconds wall clock time: 47 minutes 27.29 seconds (2847.29 seconds total)