Starting phenix.real_space_refine on Fri Mar 15 19:39:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0m_9764/03_2024/6j0m_9764.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0m_9764/03_2024/6j0m_9764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0m_9764/03_2024/6j0m_9764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0m_9764/03_2024/6j0m_9764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0m_9764/03_2024/6j0m_9764.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0m_9764/03_2024/6j0m_9764.pdb" } resolution = 3.9 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= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 7974 2.51 5 N 2208 2.21 5 O 2361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 21": "OD1" <-> "OD2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 160": "OD1" <-> "OD2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A ASP 324": "OD1" <-> "OD2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A ASP 419": "OD1" <-> "OD2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A ARG 480": "NH1" <-> "NH2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B ASP 42": "OD1" <-> "OD2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 160": "OD1" <-> "OD2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ASP 324": "OD1" <-> "OD2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B ARG 480": "NH1" <-> "NH2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "C ASP 21": "OD1" <-> "OD2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "C ASP 324": "OD1" <-> "OD2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "C TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 391": "NH1" <-> "NH2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "C TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 416": "OE1" <-> "OE2" Residue "C ASP 419": "OD1" <-> "OD2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C ARG 431": "NH1" <-> "NH2" Residue "C TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 449": "OE1" <-> "OE2" Residue "C ARG 480": "NH1" <-> "NH2" Residue "C GLU 485": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12585 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4195 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 21, 'TRANS': 513} Chain breaks: 1 Chain: "B" Number of atoms: 4195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4195 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 21, 'TRANS': 513} Chain breaks: 1 Chain: "C" Number of atoms: 4195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4195 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 21, 'TRANS': 513} Chain breaks: 1 Time building chain proxies: 6.10, per 1000 atoms: 0.48 Number of scatterers: 12585 At special positions: 0 Unit cell: (95.285, 96.406, 143.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2361 8.00 N 2208 7.00 C 7974 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: 4.26 Conformation dependent library (CDL) restraints added in 2.2 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2994 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 30 sheets defined 12.7% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 50 through 60 removed outlier: 3.680A pdb=" N GLU A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.581A pdb=" N THR A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.741A pdb=" N LEU A 165 " --> pdb=" O TRP A 161 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N CYS A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 170 " --> pdb=" O CYS A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.544A pdb=" N LYS A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 294 removed outlier: 3.594A pdb=" N GLN A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'B' and resid 50 through 60 removed outlier: 3.681A pdb=" N GLU B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 122 through 132 removed outlier: 3.582A pdb=" N THR B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 172 removed outlier: 3.742A pdb=" N LEU B 165 " --> pdb=" O TRP B 161 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS B 166 " --> pdb=" O HIS B 162 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 170 " --> pdb=" O CYS B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.543A pdb=" N LYS B 191 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 294 removed outlier: 3.594A pdb=" N GLN B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'C' and resid 50 through 60 removed outlier: 3.680A pdb=" N GLU C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 122 through 132 removed outlier: 3.582A pdb=" N THR C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 172 removed outlier: 3.741A pdb=" N LEU C 165 " --> pdb=" O TRP C 161 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N CYS C 166 " --> pdb=" O HIS C 162 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA C 170 " --> pdb=" O CYS C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.544A pdb=" N LYS C 191 " --> pdb=" O ASP C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 294 removed outlier: 3.594A pdb=" N GLN C 285 " --> pdb=" O GLY C 281 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 4.747A pdb=" N ILE A 7 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 80 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A 70 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL A 78 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE A 84 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LYS A 103 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER A 39 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA A 19 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 4.751A pdb=" N ASP C 212 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU C 301 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 325 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR C 196 " --> pdb=" O GLN C 315 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR C 317 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU C 198 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 118 Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.608A pdb=" N VAL A 185 " --> pdb=" O TRP A 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 195 through 199 removed outlier: 6.476A pdb=" N TYR A 196 " --> pdb=" O GLN A 315 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR A 317 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU A 198 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 325 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A 301 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP A 212 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 14 removed outlier: 4.747A pdb=" N ILE B 7 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 80 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU B 70 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 78 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE B 84 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LYS B 103 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER B 39 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ALA B 19 " --> pdb=" O SER B 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 237 through 243 removed outlier: 3.819A pdb=" N GLN A 237 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY A 230 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 241 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL A 228 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG A 243 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU A 226 " --> pdb=" O ARG A 243 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 227 " --> pdb=" O TRP A 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 365 through 369 removed outlier: 7.587A pdb=" N TRP A 397 " --> pdb=" O PRO A 433 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE A 435 " --> pdb=" O TRP A 397 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ARG A 399 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLY A 437 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 422 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA A 438 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N GLU A 420 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 367 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 411 through 412 Processing sheet with id=AB1, first strand: chain 'A' and resid 488 through 491 Processing sheet with id=AB2, first strand: chain 'A' and resid 461 through 462 Processing sheet with id=AB3, first strand: chain 'A' and resid 503 through 508 removed outlier: 6.174A pdb=" N LEU A 504 " --> pdb=" O ASN C 512 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N THR C 514 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 506 " --> pdb=" O THR C 514 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 510 through 515 Processing sheet with id=AB5, first strand: chain 'A' and resid 519 through 522 removed outlier: 3.510A pdb=" N ILE C 529 " --> pdb=" O ASN B 535 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 519 through 522 removed outlier: 5.632A pdb=" N GLU A 528 " --> pdb=" O MET B 521 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 527 " --> pdb=" O ASN C 535 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR C 537 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 529 " --> pdb=" O THR C 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 534 through 537 removed outlier: 3.516A pdb=" N ASN A 535 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 529 " --> pdb=" O ASN A 535 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU B 528 " --> pdb=" O MET C 521 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AB9, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.608A pdb=" N VAL B 185 " --> pdb=" O TRP B 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 195 through 199 removed outlier: 6.476A pdb=" N TYR B 196 " --> pdb=" O GLN B 315 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR B 317 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU B 198 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 325 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 301 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP B 212 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 12 through 14 removed outlier: 4.746A pdb=" N ILE C 7 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C 80 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU C 70 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL C 78 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE C 84 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LYS C 103 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER C 39 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ALA C 19 " --> pdb=" O SER C 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 237 through 243 removed outlier: 3.819A pdb=" N GLN B 237 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY B 230 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 241 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL B 228 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG B 243 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU B 226 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B 227 " --> pdb=" O TRP B 267 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 365 through 369 removed outlier: 7.587A pdb=" N TRP B 397 " --> pdb=" O PRO B 433 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE B 435 " --> pdb=" O TRP B 397 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ARG B 399 " --> pdb=" O ILE B 435 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLY B 437 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE B 422 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA B 438 " --> pdb=" O GLU B 420 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N GLU B 420 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 367 " --> pdb=" O VAL B 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 411 through 412 Processing sheet with id=AC6, first strand: chain 'B' and resid 461 through 462 Processing sheet with id=AC7, first strand: chain 'B' and resid 510 through 515 Processing sheet with id=AC8, first strand: chain 'C' and resid 116 through 118 Processing sheet with id=AC9, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.607A pdb=" N VAL C 185 " --> pdb=" O TRP C 174 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 237 through 243 removed outlier: 3.818A pdb=" N GLN C 237 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY C 230 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 241 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL C 228 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG C 243 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU C 226 " --> pdb=" O ARG C 243 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 227 " --> pdb=" O TRP C 267 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 365 through 369 removed outlier: 7.587A pdb=" N TRP C 397 " --> pdb=" O PRO C 433 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE C 435 " --> pdb=" O TRP C 397 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ARG C 399 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLY C 437 " --> pdb=" O ARG C 399 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE C 422 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA C 438 " --> pdb=" O GLU C 420 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU C 420 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 367 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 461 through 462 391 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 4.62 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: 4146 1.34 - 1.46: 2122 1.46 - 1.57: 6473 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 12807 Sorted by residual: bond pdb=" CA TRP A 267 " pdb=" CB TRP A 267 " ideal model delta sigma weight residual 1.534 1.504 0.030 1.78e-02 3.16e+03 2.82e+00 bond pdb=" CA TRP B 267 " pdb=" CB TRP B 267 " ideal model delta sigma weight residual 1.534 1.504 0.029 1.78e-02 3.16e+03 2.72e+00 bond pdb=" C ASN A 222 " pdb=" N PRO A 223 " ideal model delta sigma weight residual 1.333 1.313 0.019 1.17e-02 7.31e+03 2.70e+00 bond pdb=" C ASN C 222 " pdb=" N PRO C 223 " ideal model delta sigma weight residual 1.333 1.314 0.019 1.17e-02 7.31e+03 2.68e+00 bond pdb=" CA TRP C 267 " pdb=" CB TRP C 267 " ideal model delta sigma weight residual 1.534 1.505 0.029 1.78e-02 3.16e+03 2.66e+00 ... (remaining 12802 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.30: 217 105.30 - 112.53: 6804 112.53 - 119.75: 4124 119.75 - 126.97: 6012 126.97 - 134.20: 159 Bond angle restraints: 17316 Sorted by residual: angle pdb=" N GLY B 484 " pdb=" CA GLY B 484 " pdb=" C GLY B 484 " ideal model delta sigma weight residual 112.68 107.56 5.12 1.26e+00 6.30e-01 1.65e+01 angle pdb=" N GLY A 484 " pdb=" CA GLY A 484 " pdb=" C GLY A 484 " ideal model delta sigma weight residual 112.68 107.57 5.11 1.26e+00 6.30e-01 1.64e+01 angle pdb=" N GLY C 484 " pdb=" CA GLY C 484 " pdb=" C GLY C 484 " ideal model delta sigma weight residual 112.68 107.61 5.07 1.26e+00 6.30e-01 1.62e+01 angle pdb=" CA LYS A 235 " pdb=" CB LYS A 235 " pdb=" CG LYS A 235 " ideal model delta sigma weight residual 114.10 121.64 -7.54 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CA LYS C 235 " pdb=" CB LYS C 235 " pdb=" CG LYS C 235 " ideal model delta sigma weight residual 114.10 121.64 -7.54 2.00e+00 2.50e-01 1.42e+01 ... (remaining 17311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6825 17.97 - 35.94: 806 35.94 - 53.91: 151 53.91 - 71.89: 21 71.89 - 89.86: 15 Dihedral angle restraints: 7818 sinusoidal: 3189 harmonic: 4629 Sorted by residual: dihedral pdb=" CA GLY B 304 " pdb=" C GLY B 304 " pdb=" N ASP B 305 " pdb=" CA ASP B 305 " ideal model delta harmonic sigma weight residual -180.00 -144.82 -35.18 0 5.00e+00 4.00e-02 4.95e+01 dihedral pdb=" CA GLY A 304 " pdb=" C GLY A 304 " pdb=" N ASP A 305 " pdb=" CA ASP A 305 " ideal model delta harmonic sigma weight residual -180.00 -144.82 -35.18 0 5.00e+00 4.00e-02 4.95e+01 dihedral pdb=" CA GLY C 304 " pdb=" C GLY C 304 " pdb=" N ASP C 305 " pdb=" CA ASP C 305 " ideal model delta harmonic sigma weight residual -180.00 -144.88 -35.12 0 5.00e+00 4.00e-02 4.93e+01 ... (remaining 7815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1485 0.059 - 0.117: 410 0.117 - 0.176: 70 0.176 - 0.235: 7 0.235 - 0.293: 5 Chirality restraints: 1977 Sorted by residual: chirality pdb=" CB ILE A 91 " pdb=" CA ILE A 91 " pdb=" CG1 ILE A 91 " pdb=" CG2 ILE A 91 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE C 91 " pdb=" CA ILE C 91 " pdb=" CG1 ILE C 91 " pdb=" CG2 ILE C 91 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB ILE B 91 " pdb=" CA ILE B 91 " pdb=" CG1 ILE B 91 " pdb=" CG2 ILE B 91 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1974 not shown) Planarity restraints: 2226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 355 " -0.045 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO B 356 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 356 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 356 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 355 " 0.044 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO C 356 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 356 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 356 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 355 " -0.044 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO A 356 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " -0.036 5.00e-02 4.00e+02 ... (remaining 2223 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3407 2.81 - 3.33: 10628 3.33 - 3.85: 20037 3.85 - 4.38: 23042 4.38 - 4.90: 41234 Nonbonded interactions: 98348 Sorted by model distance: nonbonded pdb=" O LYS A 124 " pdb=" OG SER A 128 " model vdw 2.282 2.440 nonbonded pdb=" O LYS B 124 " pdb=" OG SER B 128 " model vdw 2.282 2.440 nonbonded pdb=" O LYS C 124 " pdb=" OG SER C 128 " model vdw 2.282 2.440 nonbonded pdb=" OG SER B 255 " pdb=" O ASP B 257 " model vdw 2.341 2.440 nonbonded pdb=" OG SER C 255 " pdb=" O ASP C 257 " model vdw 2.342 2.440 ... (remaining 98343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.020 Extract box with map and model: 6.350 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.370 Find NCS groups from input model: 0.710 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.007 0.047 12807 Z= 0.478 Angle : 0.980 9.902 17316 Z= 0.561 Chirality : 0.056 0.293 1977 Planarity : 0.007 0.066 2226 Dihedral : 15.907 89.858 4824 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.87 % Allowed : 12.44 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.17), residues: 1593 helix: -4.47 (0.15), residues: 159 sheet: -2.50 (0.19), residues: 525 loop : -2.47 (0.16), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 267 HIS 0.005 0.001 HIS A 407 PHE 0.023 0.002 PHE C 411 TYR 0.017 0.002 TYR B 354 ARG 0.004 0.001 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 281 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.5730 (p0) cc_final: 0.5490 (p0) REVERT: A 257 ASP cc_start: 0.8331 (m-30) cc_final: 0.8018 (m-30) REVERT: A 312 ASP cc_start: 0.8275 (p0) cc_final: 0.7893 (p0) REVERT: A 374 GLN cc_start: 0.7371 (tm-30) cc_final: 0.7102 (tm-30) REVERT: A 494 LYS cc_start: 0.7602 (pttp) cc_final: 0.7291 (ptmt) REVERT: B 218 ASP cc_start: 0.7240 (m-30) cc_final: 0.7021 (m-30) REVERT: B 257 ASP cc_start: 0.8486 (m-30) cc_final: 0.8270 (m-30) REVERT: B 269 ILE cc_start: 0.9036 (pt) cc_final: 0.8803 (mp) REVERT: B 494 LYS cc_start: 0.7472 (pttp) cc_final: 0.7200 (ptmt) REVERT: C 26 TYR cc_start: 0.8949 (m-80) cc_final: 0.8612 (m-80) REVERT: C 120 ASP cc_start: 0.6305 (p0) cc_final: 0.6087 (p0) REVERT: C 257 ASP cc_start: 0.8297 (m-30) cc_final: 0.8048 (m-30) REVERT: C 494 LYS cc_start: 0.7258 (pttp) cc_final: 0.6950 (ptmt) REVERT: C 521 MET cc_start: 0.6498 (ttm) cc_final: 0.6076 (tpp) outliers start: 12 outliers final: 3 residues processed: 287 average time/residue: 0.2698 time to fit residues: 106.5541 Evaluate side-chains 175 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 461 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 152 GLN A 222 ASN A 239 GLN A 322 GLN A 373 GLN A 428 ASN ** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN B 152 GLN B 222 ASN B 290 ASN B 322 GLN B 373 GLN B 428 ASN B 482 ASN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 GLN C 152 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN C 373 GLN C 428 ASN ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12807 Z= 0.266 Angle : 0.652 9.076 17316 Z= 0.339 Chirality : 0.046 0.150 1977 Planarity : 0.004 0.042 2226 Dihedral : 6.308 29.018 1707 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.11 % Allowed : 17.43 % Favored : 79.46 % 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: -3.09 (0.19), residues: 1593 helix: -2.31 (0.34), residues: 168 sheet: -1.97 (0.20), residues: 552 loop : -2.02 (0.18), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 267 HIS 0.003 0.001 HIS A 334 PHE 0.012 0.001 PHE B 411 TYR 0.014 0.001 TYR A 354 ARG 0.005 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 209 time to evaluate : 1.638 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.5707 (p0) cc_final: 0.5452 (p0) REVERT: A 257 ASP cc_start: 0.8229 (m-30) cc_final: 0.8011 (m-30) REVERT: A 494 LYS cc_start: 0.7612 (pttp) cc_final: 0.7309 (ptmt) REVERT: A 521 MET cc_start: 0.5852 (ttp) cc_final: 0.5554 (ttp) REVERT: A 534 ILE cc_start: 0.6072 (OUTLIER) cc_final: 0.5673 (tp) REVERT: B 358 LEU cc_start: 0.6780 (tt) cc_final: 0.6300 (tp) REVERT: B 494 LYS cc_start: 0.7530 (pttp) cc_final: 0.7303 (ptmt) REVERT: B 534 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6320 (tp) REVERT: C 26 TYR cc_start: 0.8976 (m-80) cc_final: 0.8619 (m-80) REVERT: C 120 ASP cc_start: 0.6009 (p0) cc_final: 0.5719 (p0) REVERT: C 358 LEU cc_start: 0.6591 (tt) cc_final: 0.6135 (tp) REVERT: C 521 MET cc_start: 0.6478 (ttm) cc_final: 0.6162 (tpp) REVERT: C 534 ILE cc_start: 0.5875 (OUTLIER) cc_final: 0.5401 (tp) outliers start: 43 outliers final: 28 residues processed: 235 average time/residue: 0.2343 time to fit residues: 80.3435 Evaluate side-chains 193 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 308 TYR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 174 TRP Chi-restraints excluded: chain C residue 215 TRP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 534 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 156 optimal weight: 30.0000 chunk 128 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN C 337 ASN ** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12807 Z= 0.379 Angle : 0.690 7.470 17316 Z= 0.357 Chirality : 0.048 0.163 1977 Planarity : 0.004 0.045 2226 Dihedral : 6.275 33.181 1707 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 5.28 % Allowed : 19.60 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.19), residues: 1593 helix: -1.88 (0.37), residues: 183 sheet: -1.72 (0.21), residues: 549 loop : -2.06 (0.18), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 267 HIS 0.003 0.001 HIS A 334 PHE 0.013 0.002 PHE B 163 TYR 0.015 0.002 TYR A 354 ARG 0.004 0.001 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 172 time to evaluate : 1.182 Fit side-chains REVERT: A 123 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: A 257 ASP cc_start: 0.8347 (m-30) cc_final: 0.8130 (m-30) REVERT: A 315 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8145 (pt0) REVERT: A 358 LEU cc_start: 0.7059 (tt) cc_final: 0.6772 (tp) REVERT: A 534 ILE cc_start: 0.6425 (OUTLIER) cc_final: 0.6017 (tp) REVERT: B 315 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: B 358 LEU cc_start: 0.6873 (tt) cc_final: 0.6371 (tp) REVERT: B 494 LYS cc_start: 0.7762 (pttp) cc_final: 0.7216 (ptmt) REVERT: B 534 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6852 (tp) REVERT: C 26 TYR cc_start: 0.8930 (m-80) cc_final: 0.8553 (m-80) REVERT: C 120 ASP cc_start: 0.6002 (p0) cc_final: 0.5756 (p0) REVERT: C 321 SER cc_start: 0.8712 (p) cc_final: 0.8451 (m) REVERT: C 358 LEU cc_start: 0.6874 (tt) cc_final: 0.6457 (tp) REVERT: C 373 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7567 (mp10) REVERT: C 534 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6120 (tp) outliers start: 73 outliers final: 51 residues processed: 228 average time/residue: 0.2142 time to fit residues: 72.5223 Evaluate side-chains 213 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 155 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 308 TYR Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 174 TRP Chi-restraints excluded: chain C residue 215 TRP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 534 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 chunk 153 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 290 ASN A 322 GLN ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12807 Z= 0.178 Angle : 0.573 9.453 17316 Z= 0.293 Chirality : 0.044 0.149 1977 Planarity : 0.003 0.036 2226 Dihedral : 5.691 31.989 1707 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.21 % Allowed : 21.48 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.20), residues: 1593 helix: -1.54 (0.37), residues: 183 sheet: -1.43 (0.22), residues: 549 loop : -1.84 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 215 HIS 0.003 0.001 HIS B 162 PHE 0.014 0.001 PHE B 411 TYR 0.009 0.001 TYR A 354 ARG 0.003 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 189 time to evaluate : 1.437 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: A 494 LYS cc_start: 0.7543 (pttp) cc_final: 0.7158 (ptmt) REVERT: B 315 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8173 (pt0) REVERT: B 358 LEU cc_start: 0.6521 (tt) cc_final: 0.5990 (tp) REVERT: B 494 LYS cc_start: 0.7590 (pttp) cc_final: 0.7320 (ptmt) REVERT: B 534 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6714 (tp) REVERT: C 26 TYR cc_start: 0.8830 (m-80) cc_final: 0.8541 (m-80) REVERT: C 94 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8449 (mtmt) REVERT: C 120 ASP cc_start: 0.5994 (p0) cc_final: 0.5657 (p0) outliers start: 72 outliers final: 46 residues processed: 238 average time/residue: 0.2209 time to fit residues: 78.2929 Evaluate side-chains 214 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 164 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 308 TYR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 174 TRP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 215 TRP Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN C 491 GLN C 492 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12807 Z= 0.400 Angle : 0.694 10.277 17316 Z= 0.355 Chirality : 0.048 0.162 1977 Planarity : 0.004 0.039 2226 Dihedral : 6.053 34.998 1707 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.78 % Allowed : 23.79 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.20), residues: 1593 helix: -1.36 (0.39), residues: 183 sheet: -1.52 (0.22), residues: 549 loop : -1.97 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 267 HIS 0.004 0.001 HIS C 334 PHE 0.014 0.002 PHE B 163 TYR 0.011 0.002 TYR A 354 ARG 0.004 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 158 time to evaluate : 1.657 Fit side-chains REVERT: A 123 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: A 534 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.6073 (tp) REVERT: B 315 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8265 (pt0) REVERT: B 358 LEU cc_start: 0.6785 (tt) cc_final: 0.6374 (tp) REVERT: B 534 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6816 (tp) REVERT: C 26 TYR cc_start: 0.8890 (m-80) cc_final: 0.8587 (m-80) REVERT: C 120 ASP cc_start: 0.6022 (p0) cc_final: 0.5761 (p0) REVERT: C 373 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: C 534 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6470 (tp) outliers start: 80 outliers final: 66 residues processed: 211 average time/residue: 0.2101 time to fit residues: 66.9044 Evaluate side-chains 219 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 147 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 TYR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 174 TRP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 215 TRP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 534 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12807 Z= 0.261 Angle : 0.614 9.272 17316 Z= 0.313 Chirality : 0.045 0.154 1977 Planarity : 0.003 0.035 2226 Dihedral : 5.814 33.719 1707 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.44 % Allowed : 24.51 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.20), residues: 1593 helix: -1.24 (0.39), residues: 183 sheet: -1.37 (0.22), residues: 549 loop : -1.88 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 215 HIS 0.003 0.001 HIS B 162 PHE 0.013 0.002 PHE A 411 TYR 0.014 0.001 TYR A 282 ARG 0.003 0.000 ARG C 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 161 time to evaluate : 1.557 Fit side-chains REVERT: A 123 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: A 315 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8209 (pt0) REVERT: A 321 SER cc_start: 0.8663 (p) cc_final: 0.8453 (m) REVERT: A 534 ILE cc_start: 0.6298 (OUTLIER) cc_final: 0.5892 (tp) REVERT: B 153 MET cc_start: 0.8346 (mmt) cc_final: 0.7499 (tpp) REVERT: B 315 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: B 358 LEU cc_start: 0.6582 (tt) cc_final: 0.6258 (tp) REVERT: B 494 LYS cc_start: 0.7632 (pttp) cc_final: 0.7060 (ptmt) REVERT: B 534 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.6861 (tp) REVERT: C 26 TYR cc_start: 0.8870 (m-80) cc_final: 0.8623 (m-80) REVERT: C 120 ASP cc_start: 0.6003 (p0) cc_final: 0.5680 (p0) REVERT: C 153 MET cc_start: 0.8332 (tpt) cc_final: 0.8006 (tpt) REVERT: C 308 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: C 373 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: C 534 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.6149 (tp) outliers start: 89 outliers final: 71 residues processed: 222 average time/residue: 0.2137 time to fit residues: 71.8041 Evaluate side-chains 237 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 158 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 TYR Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 174 TRP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 215 TRP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 308 TYR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 534 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12807 Z= 0.340 Angle : 0.659 9.405 17316 Z= 0.335 Chirality : 0.047 0.161 1977 Planarity : 0.004 0.036 2226 Dihedral : 5.903 33.845 1707 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 6.72 % Allowed : 24.95 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.20), residues: 1593 helix: -1.21 (0.38), residues: 183 sheet: -1.40 (0.22), residues: 549 loop : -1.93 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 215 HIS 0.003 0.001 HIS C 334 PHE 0.012 0.002 PHE B 411 TYR 0.016 0.002 TYR A 282 ARG 0.003 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 157 time to evaluate : 1.599 Fit side-chains REVERT: A 123 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: A 534 ILE cc_start: 0.6448 (OUTLIER) cc_final: 0.6065 (tp) REVERT: B 214 TYR cc_start: 0.8735 (t80) cc_final: 0.8045 (t80) REVERT: B 315 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8245 (pt0) REVERT: B 534 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.6884 (tp) REVERT: C 26 TYR cc_start: 0.8890 (m-80) cc_final: 0.8645 (m-80) REVERT: C 94 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8344 (mtmt) REVERT: C 120 ASP cc_start: 0.5927 (p0) cc_final: 0.5630 (p0) REVERT: C 308 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: C 373 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: C 534 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6713 (tp) outliers start: 93 outliers final: 77 residues processed: 225 average time/residue: 0.2014 time to fit residues: 69.2276 Evaluate side-chains 237 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 152 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 TYR Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 174 TRP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 215 TRP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 308 TYR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 534 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12807 Z= 0.315 Angle : 0.650 9.172 17316 Z= 0.329 Chirality : 0.046 0.157 1977 Planarity : 0.003 0.036 2226 Dihedral : 5.888 33.947 1707 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 7.01 % Allowed : 24.95 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.20), residues: 1593 helix: -1.17 (0.38), residues: 183 sheet: -1.39 (0.22), residues: 549 loop : -1.93 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 215 HIS 0.004 0.001 HIS C 334 PHE 0.013 0.002 PHE A 411 TYR 0.015 0.001 TYR A 282 ARG 0.003 0.000 ARG C 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 159 time to evaluate : 1.507 Fit side-chains REVERT: A 123 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: A 315 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8403 (pt0) REVERT: A 534 ILE cc_start: 0.6421 (OUTLIER) cc_final: 0.6033 (tp) REVERT: B 315 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: B 534 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6851 (tp) REVERT: C 26 TYR cc_start: 0.8892 (m-80) cc_final: 0.8634 (m-80) REVERT: C 94 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8341 (mtmt) REVERT: C 120 ASP cc_start: 0.5924 (p0) cc_final: 0.5618 (p0) REVERT: C 308 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: C 373 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7586 (mp10) REVERT: C 534 ILE cc_start: 0.7119 (OUTLIER) cc_final: 0.6692 (tp) outliers start: 97 outliers final: 79 residues processed: 230 average time/residue: 0.2084 time to fit residues: 72.5312 Evaluate side-chains 241 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 153 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 TYR Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 174 TRP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 215 TRP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 308 TYR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 535 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12807 Z= 0.315 Angle : 0.649 9.127 17316 Z= 0.329 Chirality : 0.046 0.159 1977 Planarity : 0.003 0.036 2226 Dihedral : 5.863 34.053 1707 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 6.51 % Allowed : 25.74 % Favored : 67.75 % 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: -2.51 (0.20), residues: 1593 helix: -1.08 (0.39), residues: 183 sheet: -1.45 (0.22), residues: 555 loop : -1.92 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 215 HIS 0.009 0.001 HIS C 162 PHE 0.013 0.002 PHE B 411 TYR 0.016 0.002 TYR A 432 ARG 0.007 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 163 time to evaluate : 1.504 Fit side-chains REVERT: A 123 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: A 482 ASN cc_start: 0.7895 (t0) cc_final: 0.7451 (t0) REVERT: A 534 ILE cc_start: 0.6406 (OUTLIER) cc_final: 0.6019 (tp) REVERT: B 315 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8236 (pt0) REVERT: B 534 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.6813 (tp) REVERT: C 26 TYR cc_start: 0.8881 (m-80) cc_final: 0.8632 (m-80) REVERT: C 94 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8357 (mtmt) REVERT: C 120 ASP cc_start: 0.5935 (p0) cc_final: 0.5640 (p0) REVERT: C 308 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: C 373 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7490 (mp10) REVERT: C 534 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6722 (tp) outliers start: 90 outliers final: 80 residues processed: 227 average time/residue: 0.2266 time to fit residues: 77.9607 Evaluate side-chains 246 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 158 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 TYR Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 174 TRP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 215 TRP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 308 TYR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 535 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12807 Z= 0.362 Angle : 0.682 9.412 17316 Z= 0.344 Chirality : 0.047 0.161 1977 Planarity : 0.004 0.036 2226 Dihedral : 5.954 33.919 1707 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 6.65 % Allowed : 25.38 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.20), residues: 1593 helix: -1.07 (0.38), residues: 183 sheet: -1.48 (0.22), residues: 555 loop : -1.95 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 215 HIS 0.008 0.001 HIS C 162 PHE 0.013 0.002 PHE A 411 TYR 0.016 0.002 TYR A 282 ARG 0.005 0.000 ARG B 399 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 159 time to evaluate : 1.479 Fit side-chains REVERT: A 123 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: A 482 ASN cc_start: 0.7956 (t0) cc_final: 0.7459 (t0) REVERT: A 534 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.5975 (tp) REVERT: B 315 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: B 534 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.6908 (tp) REVERT: C 26 TYR cc_start: 0.8884 (m-80) cc_final: 0.8639 (m-80) REVERT: C 120 ASP cc_start: 0.5965 (p0) cc_final: 0.5677 (p0) REVERT: C 162 HIS cc_start: 0.7501 (m90) cc_final: 0.7120 (m90) REVERT: C 308 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: C 373 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7483 (mp10) REVERT: C 534 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6700 (tp) outliers start: 92 outliers final: 80 residues processed: 224 average time/residue: 0.2118 time to fit residues: 72.2803 Evaluate side-chains 243 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 156 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 174 TRP Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 TYR Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 174 TRP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 174 TRP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 215 TRP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 308 TYR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 454 ASN Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 486 ASN Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 535 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 126 optimal weight: 0.0570 chunk 52 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.099010 restraints weight = 21191.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.100702 restraints weight = 14814.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101934 restraints weight = 11303.874| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12807 Z= 0.200 Angle : 0.603 8.960 17316 Z= 0.302 Chirality : 0.045 0.152 1977 Planarity : 0.003 0.034 2226 Dihedral : 5.576 31.834 1707 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.00 % Allowed : 26.39 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.20), residues: 1593 helix: -0.92 (0.38), residues: 183 sheet: -1.27 (0.23), residues: 549 loop : -1.82 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 215 HIS 0.006 0.001 HIS C 162 PHE 0.015 0.001 PHE A 411 TYR 0.013 0.001 TYR A 282 ARG 0.006 0.000 ARG B 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.78 seconds wall clock time: 41 minutes 58.47 seconds (2518.47 seconds total)