Starting phenix.real_space_refine on Sat Dec 9 23:00:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0m_9764/12_2023/6j0m_9764.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0m_9764/12_2023/6j0m_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_9764/12_2023/6j0m_9764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0m_9764/12_2023/6j0m_9764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0m_9764/12_2023/6j0m_9764.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0m_9764/12_2023/6j0m_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.26, per 1000 atoms: 0.58 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: 4.64 Conformation dependent library (CDL) restraints added in 2.5 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: 1.64 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: 4.41 Time building geometry restraints manager: 5.09 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.760 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.000 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.170 ------------------------------------------------------------------------------- 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 : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 287 average time/residue: 0.2890 time to fit residues: 114.5491 Evaluate side-chains 171 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 1.560 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1148 time to fit residues: 2.7702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 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: 2.7990 ------------------------------------------------------------------------------- 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 482 ASN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN B 152 GLN B 220 GLN B 222 ASN B 290 ASN B 322 GLN B 373 GLN B 428 ASN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12807 Z= 0.230 Angle : 0.633 9.714 17316 Z= 0.328 Chirality : 0.045 0.148 1977 Planarity : 0.004 0.041 2226 Dihedral : 6.090 23.151 1704 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.68 % Allowed : 17.50 % Favored : 79.83 % 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: -3.03 (0.19), residues: 1593 helix: -2.30 (0.34), residues: 168 sheet: -1.93 (0.21), residues: 540 loop : -1.98 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 267 HIS 0.003 0.001 HIS A 334 PHE 0.012 0.001 PHE B 411 TYR 0.013 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 248 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 1.693 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 25 residues processed: 232 average time/residue: 0.2395 time to fit residues: 81.9115 Evaluate side-chains 188 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 1.463 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1249 time to fit residues: 7.6077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 156 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 322 GLN ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 HIS ** 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 337 ASN C 491 GLN C 492 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12807 Z= 0.319 Angle : 0.658 7.902 17316 Z= 0.340 Chirality : 0.047 0.156 1977 Planarity : 0.004 0.043 2226 Dihedral : 5.957 26.350 1704 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.90 % Allowed : 19.60 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.19), residues: 1593 helix: -1.84 (0.37), residues: 183 sheet: -1.65 (0.21), residues: 549 loop : -1.96 (0.18), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 267 HIS 0.003 0.001 HIS A 334 PHE 0.012 0.002 PHE B 411 TYR 0.014 0.002 TYR A 354 ARG 0.006 0.001 ARG A 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 233 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 179 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 28 residues processed: 224 average time/residue: 0.2295 time to fit residues: 76.2355 Evaluate side-chains 184 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1267 time to fit residues: 8.4918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 145 optimal weight: 0.0370 chunk 153 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 322 GLN B 322 GLN ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12807 Z= 0.131 Angle : 0.556 9.399 17316 Z= 0.284 Chirality : 0.044 0.154 1977 Planarity : 0.003 0.033 2226 Dihedral : 5.338 22.038 1704 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.02 % Allowed : 21.98 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.20), residues: 1593 helix: -1.10 (0.39), residues: 165 sheet: -1.22 (0.23), residues: 516 loop : -1.61 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 342 HIS 0.003 0.001 HIS A 440 PHE 0.014 0.001 PHE A 411 TYR 0.009 0.001 TYR A 372 ARG 0.004 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 248 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 220 time to evaluate : 1.523 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 238 average time/residue: 0.2422 time to fit residues: 85.5998 Evaluate side-chains 189 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 177 time to evaluate : 1.520 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1539 time to fit residues: 5.2473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 114 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN ** 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 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 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 12807 Z= 0.436 Angle : 0.732 9.308 17316 Z= 0.373 Chirality : 0.049 0.182 1977 Planarity : 0.004 0.042 2226 Dihedral : 5.952 28.553 1704 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.40 % Allowed : 25.31 % Favored : 71.29 % 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: -2.55 (0.20), residues: 1593 helix: -1.38 (0.39), residues: 183 sheet: -1.44 (0.23), residues: 537 loop : -1.92 (0.18), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 267 HIS 0.004 0.001 HIS C 334 PHE 0.015 0.002 PHE A 300 TYR 0.015 0.002 TYR C 26 ARG 0.005 0.001 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 221 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 174 time to evaluate : 1.663 Fit side-chains outliers start: 47 outliers final: 30 residues processed: 202 average time/residue: 0.2238 time to fit residues: 68.0419 Evaluate side-chains 181 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1339 time to fit residues: 9.0523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 30.0000 chunk 80 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN ** A 290 ASN ** 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 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 C 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3171 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= 0.282 Angle : 0.643 8.740 17316 Z= 0.325 Chirality : 0.047 0.151 1977 Planarity : 0.003 0.038 2226 Dihedral : 5.734 27.258 1704 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.68 % Allowed : 26.03 % Favored : 71.29 % 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: -2.42 (0.20), residues: 1593 helix: -1.27 (0.39), residues: 183 sheet: -1.21 (0.23), residues: 519 loop : -1.94 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 215 HIS 0.004 0.001 HIS B 162 PHE 0.013 0.002 PHE C 411 TYR 0.016 0.001 TYR A 282 ARG 0.003 0.000 ARG C 431 *********************** 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 201 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 1.575 Fit side-chains outliers start: 37 outliers final: 26 residues processed: 191 average time/residue: 0.2217 time to fit residues: 64.4654 Evaluate side-chains 177 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1506 time to fit residues: 8.8741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 112 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3296 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= 0.346 Angle : 0.685 9.280 17316 Z= 0.344 Chirality : 0.048 0.178 1977 Planarity : 0.004 0.038 2226 Dihedral : 5.798 27.988 1704 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.53 % Allowed : 26.83 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.20), residues: 1593 helix: -1.22 (0.38), residues: 183 sheet: -1.27 (0.23), residues: 537 loop : -1.96 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 215 HIS 0.004 0.001 HIS B 162 PHE 0.012 0.002 PHE C 411 TYR 0.018 0.002 TYR A 282 ARG 0.005 0.000 ARG B 167 *********************** 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 197 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 1.725 Fit side-chains outliers start: 35 outliers final: 27 residues processed: 187 average time/residue: 0.2463 time to fit residues: 70.0703 Evaluate side-chains 182 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.561 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1210 time to fit residues: 8.1615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 146 optimal weight: 0.0050 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 220 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN ** A 512 ASN ** 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 441 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12807 Z= 0.138 Angle : 0.589 8.309 17316 Z= 0.291 Chirality : 0.044 0.155 1977 Planarity : 0.003 0.034 2226 Dihedral : 5.210 22.606 1704 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.08 % Allowed : 27.77 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.20), residues: 1593 helix: -1.05 (0.37), residues: 183 sheet: -0.99 (0.23), residues: 531 loop : -1.81 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 174 HIS 0.004 0.001 HIS B 162 PHE 0.016 0.001 PHE C 411 TYR 0.010 0.001 TYR A 282 ARG 0.006 0.000 ARG C 167 *********************** 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 217 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 1.599 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 209 average time/residue: 0.2432 time to fit residues: 74.8200 Evaluate side-chains 173 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.485 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1244 time to fit residues: 4.1124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 0.0060 chunk 135 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 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 285 GLN B 337 ASN ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12807 Z= 0.266 Angle : 0.647 8.769 17316 Z= 0.321 Chirality : 0.046 0.168 1977 Planarity : 0.003 0.035 2226 Dihedral : 5.376 24.668 1704 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.37 % Allowed : 27.98 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.20), residues: 1593 helix: -0.87 (0.38), residues: 183 sheet: -1.09 (0.23), residues: 537 loop : -1.82 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 267 HIS 0.014 0.001 HIS A 150 PHE 0.013 0.002 PHE C 411 TYR 0.015 0.001 TYR A 282 ARG 0.004 0.000 ARG C 167 *********************** 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 185 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 1.628 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 180 average time/residue: 0.2373 time to fit residues: 63.9978 Evaluate side-chains 173 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1691 time to fit residues: 5.4071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 104 optimal weight: 20.0000 chunk 158 optimal weight: 0.4980 chunk 145 optimal weight: 0.0270 chunk 126 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 overall best weight: 2.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 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 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12807 Z= 0.182 Angle : 0.604 8.286 17316 Z= 0.298 Chirality : 0.045 0.228 1977 Planarity : 0.003 0.034 2226 Dihedral : 5.191 23.319 1704 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.43 % Allowed : 28.63 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.21), residues: 1593 helix: -0.22 (0.40), residues: 165 sheet: -0.98 (0.23), residues: 528 loop : -1.58 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 342 HIS 0.003 0.001 HIS B 162 PHE 0.015 0.001 PHE C 411 TYR 0.012 0.001 TYR A 282 ARG 0.004 0.000 ARG A 431 ********************** 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 186 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 180 time to evaluate : 1.646 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 184 average time/residue: 0.2346 time to fit residues: 64.7625 Evaluate side-chains 170 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 167 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1183 time to fit residues: 2.8933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 129 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 ASN ** A 491 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 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.102325 restraints weight = 20813.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.104064 restraints weight = 14431.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.105311 restraints weight = 10933.765| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12807 Z= 0.181 Angle : 0.601 8.327 17316 Z= 0.297 Chirality : 0.045 0.236 1977 Planarity : 0.003 0.032 2226 Dihedral : 5.126 22.478 1704 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.14 % Allowed : 29.43 % 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: -1.94 (0.20), residues: 1593 helix: -0.54 (0.38), residues: 183 sheet: -0.90 (0.23), residues: 525 loop : -1.71 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 215 HIS 0.006 0.001 HIS A 150 PHE 0.015 0.001 PHE B 411 TYR 0.012 0.001 TYR A 282 ARG 0.003 0.000 ARG C 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2401.47 seconds wall clock time: 45 minutes 6.01 seconds (2706.01 seconds total)