Starting phenix.real_space_refine on Mon Feb 19 01:36:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwb_30880/02_2024/7dwb_30880.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwb_30880/02_2024/7dwb_30880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwb_30880/02_2024/7dwb_30880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwb_30880/02_2024/7dwb_30880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwb_30880/02_2024/7dwb_30880.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwb_30880/02_2024/7dwb_30880.pdb" } resolution = 3.15 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= 0.034 sd= 0.155 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 140 5.16 5 C 15323 2.51 5 N 3745 2.21 5 O 4256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E GLU 344": "OE1" <-> "OE2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F GLU 344": "OE1" <-> "OE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G GLU 344": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23464 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3352 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3352 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3352 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3352 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3352 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3352 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3352 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 12.63, per 1000 atoms: 0.54 Number of scatterers: 23464 At special positions: 0 Unit cell: (119.88, 120.96, 137.16, 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 140 16.00 O 4256 8.00 N 3745 7.00 C 15323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 254 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 254 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 273 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 254 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 273 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 254 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 273 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 254 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 273 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 254 " distance=2.03 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: 10.88 Conformation dependent library (CDL) restraints added in 4.1 seconds 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5656 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 7 sheets defined 53.7% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.558A pdb=" N LEU A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 62 Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.985A pdb=" N LEU A 105 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.502A pdb=" N LEU A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 160 removed outlier: 4.072A pdb=" N ALA A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Proline residue: A 133 - end of helix removed outlier: 3.526A pdb=" N SER A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 154 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 164 removed outlier: 3.680A pdb=" N ASP A 164 " --> pdb=" O ARG A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 202 through 211 removed outlier: 4.133A pdb=" N GLN A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 247 removed outlier: 3.785A pdb=" N CYS A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 removed outlier: 4.174A pdb=" N ASN A 263 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 302 removed outlier: 3.532A pdb=" N LEU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.204A pdb=" N VAL A 316 " --> pdb=" O VAL A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.789A pdb=" N LYS A 363 " --> pdb=" O GLU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 381 removed outlier: 4.101A pdb=" N MET A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 381 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.548A pdb=" N GLU A 406 " --> pdb=" O GLN A 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.557A pdb=" N LEU B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 62 Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.985A pdb=" N LEU B 105 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.502A pdb=" N LEU B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 160 removed outlier: 4.073A pdb=" N ALA B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Proline residue: B 133 - end of helix removed outlier: 3.527A pdb=" N SER B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP B 147 " --> pdb=" O MET B 143 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 154 " --> pdb=" O TYR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 164 removed outlier: 3.680A pdb=" N ASP B 164 " --> pdb=" O ARG B 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 161 through 164' Processing helix chain 'B' and resid 202 through 211 removed outlier: 4.133A pdb=" N GLN B 206 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 247 removed outlier: 3.785A pdb=" N CYS B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.173A pdb=" N ASN B 263 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 302 removed outlier: 3.532A pdb=" N LEU B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 313 through 318 removed outlier: 4.203A pdb=" N VAL B 316 " --> pdb=" O VAL B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.789A pdb=" N LYS B 363 " --> pdb=" O GLU B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 381 removed outlier: 4.101A pdb=" N MET B 380 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.548A pdb=" N GLU B 406 " --> pdb=" O GLN B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.558A pdb=" N LEU C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 62 Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.986A pdb=" N LEU C 105 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.501A pdb=" N LEU C 114 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 160 removed outlier: 4.072A pdb=" N ALA C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Proline residue: C 133 - end of helix removed outlier: 3.526A pdb=" N SER C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP C 147 " --> pdb=" O MET C 143 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 154 " --> pdb=" O TYR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 164 removed outlier: 3.681A pdb=" N ASP C 164 " --> pdb=" O ARG C 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 161 through 164' Processing helix chain 'C' and resid 202 through 211 removed outlier: 4.133A pdb=" N GLN C 206 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 247 removed outlier: 3.786A pdb=" N CYS C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 264 removed outlier: 4.173A pdb=" N ASN C 263 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 302 removed outlier: 3.531A pdb=" N LEU C 283 " --> pdb=" O GLY C 279 " (cutoff:3.500A) Proline residue: C 297 - end of helix Processing helix chain 'C' and resid 313 through 318 removed outlier: 4.204A pdb=" N VAL C 316 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS C 354 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 363 removed outlier: 3.789A pdb=" N LYS C 363 " --> pdb=" O GLU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 381 removed outlier: 4.100A pdb=" N MET C 380 " --> pdb=" O ASN C 377 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 381 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.548A pdb=" N GLU C 406 " --> pdb=" O GLN C 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.558A pdb=" N LEU D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 62 Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.986A pdb=" N LEU D 105 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.502A pdb=" N LEU D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 160 removed outlier: 4.072A pdb=" N ALA D 132 " --> pdb=" O ARG D 128 " (cutoff:3.500A) Proline residue: D 133 - end of helix removed outlier: 3.527A pdb=" N SER D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP D 147 " --> pdb=" O MET D 143 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 164 removed outlier: 3.680A pdb=" N ASP D 164 " --> pdb=" O ARG D 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 164' Processing helix chain 'D' and resid 202 through 211 removed outlier: 4.133A pdb=" N GLN D 206 " --> pdb=" O PRO D 202 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 247 removed outlier: 3.785A pdb=" N CYS D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 4.174A pdb=" N ASN D 263 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 302 removed outlier: 3.532A pdb=" N LEU D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Proline residue: D 297 - end of helix Processing helix chain 'D' and resid 313 through 318 removed outlier: 4.204A pdb=" N VAL D 316 " --> pdb=" O VAL D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS D 354 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 363 removed outlier: 3.788A pdb=" N LYS D 363 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 381 removed outlier: 4.101A pdb=" N MET D 380 " --> pdb=" O ASN D 377 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 381 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 removed outlier: 3.548A pdb=" N GLU D 406 " --> pdb=" O GLN D 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.558A pdb=" N LEU E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 62 Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.985A pdb=" N LEU E 105 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 120 removed outlier: 3.501A pdb=" N LEU E 114 " --> pdb=" O PRO E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 160 removed outlier: 4.072A pdb=" N ALA E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Proline residue: E 133 - end of helix removed outlier: 3.526A pdb=" N SER E 137 " --> pdb=" O PRO E 133 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP E 147 " --> pdb=" O MET E 143 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE E 154 " --> pdb=" O TYR E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 164 removed outlier: 3.680A pdb=" N ASP E 164 " --> pdb=" O ARG E 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'E' and resid 202 through 211 removed outlier: 4.134A pdb=" N GLN E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 247 removed outlier: 3.785A pdb=" N CYS E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 264 removed outlier: 4.174A pdb=" N ASN E 263 " --> pdb=" O ILE E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 302 removed outlier: 3.533A pdb=" N LEU E 283 " --> pdb=" O GLY E 279 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 313 through 318 removed outlier: 4.203A pdb=" N VAL E 316 " --> pdb=" O VAL E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 347 Processing helix chain 'E' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS E 354 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 363 removed outlier: 3.788A pdb=" N LYS E 363 " --> pdb=" O GLU E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 381 removed outlier: 4.101A pdb=" N MET E 380 " --> pdb=" O ASN E 377 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE E 381 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.549A pdb=" N GLU E 406 " --> pdb=" O GLN E 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 13 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.557A pdb=" N LEU F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 62 Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.985A pdb=" N LEU F 105 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 120 removed outlier: 3.502A pdb=" N LEU F 114 " --> pdb=" O PRO F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 160 removed outlier: 4.072A pdb=" N ALA F 132 " --> pdb=" O ARG F 128 " (cutoff:3.500A) Proline residue: F 133 - end of helix removed outlier: 3.527A pdb=" N SER F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP F 147 " --> pdb=" O MET F 143 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS F 148 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE F 154 " --> pdb=" O TYR F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 164 removed outlier: 3.680A pdb=" N ASP F 164 " --> pdb=" O ARG F 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 161 through 164' Processing helix chain 'F' and resid 202 through 211 removed outlier: 4.133A pdb=" N GLN F 206 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 247 removed outlier: 3.785A pdb=" N CYS F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 264 removed outlier: 4.174A pdb=" N ASN F 263 " --> pdb=" O ILE F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 302 removed outlier: 3.531A pdb=" N LEU F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Proline residue: F 297 - end of helix Processing helix chain 'F' and resid 313 through 318 removed outlier: 4.203A pdb=" N VAL F 316 " --> pdb=" O VAL F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 347 Processing helix chain 'F' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS F 354 " --> pdb=" O VAL F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 363 removed outlier: 3.789A pdb=" N LYS F 363 " --> pdb=" O GLU F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 381 removed outlier: 4.101A pdb=" N MET F 380 " --> pdb=" O ASN F 377 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE F 381 " --> pdb=" O LEU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 407 removed outlier: 3.548A pdb=" N GLU F 406 " --> pdb=" O GLN F 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 13 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.557A pdb=" N LEU G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 62 Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 102 through 106 removed outlier: 3.986A pdb=" N LEU G 105 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 120 removed outlier: 3.502A pdb=" N LEU G 114 " --> pdb=" O PRO G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 160 removed outlier: 4.072A pdb=" N ALA G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) Proline residue: G 133 - end of helix removed outlier: 3.527A pdb=" N SER G 137 " --> pdb=" O PRO G 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP G 147 " --> pdb=" O MET G 143 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS G 148 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE G 154 " --> pdb=" O TYR G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 164 removed outlier: 3.680A pdb=" N ASP G 164 " --> pdb=" O ARG G 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 161 through 164' Processing helix chain 'G' and resid 202 through 211 removed outlier: 4.133A pdb=" N GLN G 206 " --> pdb=" O PRO G 202 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 247 removed outlier: 3.785A pdb=" N CYS G 224 " --> pdb=" O LYS G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 264 removed outlier: 4.174A pdb=" N ASN G 263 " --> pdb=" O ILE G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 302 removed outlier: 3.532A pdb=" N LEU G 283 " --> pdb=" O GLY G 279 " (cutoff:3.500A) Proline residue: G 297 - end of helix Processing helix chain 'G' and resid 313 through 318 removed outlier: 4.203A pdb=" N VAL G 316 " --> pdb=" O VAL G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 347 Processing helix chain 'G' and resid 350 through 357 removed outlier: 3.886A pdb=" N LYS G 354 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 363 removed outlier: 3.789A pdb=" N LYS G 363 " --> pdb=" O GLU G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 381 removed outlier: 4.101A pdb=" N MET G 380 " --> pdb=" O ASN G 377 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE G 381 " --> pdb=" O LEU G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 407 removed outlier: 3.548A pdb=" N GLU G 406 " --> pdb=" O GLN G 403 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.329A pdb=" N GLN A 272 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 67 removed outlier: 4.330A pdb=" N GLN B 272 " --> pdb=" O PHE B 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 67 removed outlier: 4.330A pdb=" N GLN C 272 " --> pdb=" O PHE C 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 67 removed outlier: 4.330A pdb=" N GLN D 272 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 67 removed outlier: 4.330A pdb=" N GLN E 272 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 67 removed outlier: 4.329A pdb=" N GLN F 272 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.329A pdb=" N GLN G 272 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2667 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: 6.08 Time building geometry restraints manager: 11.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7245 1.34 - 1.46: 5079 1.46 - 1.58: 11455 1.58 - 1.69: 7 1.69 - 1.81: 203 Bond restraints: 23989 Sorted by residual: bond pdb=" C VAL C 305 " pdb=" N PRO C 306 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.18e+00 bond pdb=" C VAL D 305 " pdb=" N PRO D 306 " ideal model delta sigma weight residual 1.334 1.375 -0.042 2.34e-02 1.83e+03 3.15e+00 bond pdb=" C VAL G 305 " pdb=" N PRO G 306 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.11e+00 bond pdb=" C VAL F 305 " pdb=" N PRO F 306 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.11e+00 bond pdb=" C VAL B 305 " pdb=" N PRO B 306 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.10e+00 ... (remaining 23984 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.93: 616 106.93 - 113.71: 13375 113.71 - 120.50: 9572 120.50 - 127.28: 8714 127.28 - 134.07: 252 Bond angle restraints: 32529 Sorted by residual: angle pdb=" N ARG B 166 " pdb=" CA ARG B 166 " pdb=" C ARG B 166 " ideal model delta sigma weight residual 114.56 109.68 4.88 1.27e+00 6.20e-01 1.48e+01 angle pdb=" N ARG C 166 " pdb=" CA ARG C 166 " pdb=" C ARG C 166 " ideal model delta sigma weight residual 114.56 109.69 4.87 1.27e+00 6.20e-01 1.47e+01 angle pdb=" N ARG D 166 " pdb=" CA ARG D 166 " pdb=" C ARG D 166 " ideal model delta sigma weight residual 114.56 109.70 4.86 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N ARG A 166 " pdb=" CA ARG A 166 " pdb=" C ARG A 166 " ideal model delta sigma weight residual 114.56 109.71 4.85 1.27e+00 6.20e-01 1.46e+01 angle pdb=" N ARG G 166 " pdb=" CA ARG G 166 " pdb=" C ARG G 166 " ideal model delta sigma weight residual 114.56 109.72 4.84 1.27e+00 6.20e-01 1.46e+01 ... (remaining 32524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 12861 16.60 - 33.20: 1349 33.20 - 49.80: 238 49.80 - 66.40: 7 66.40 - 83.00: 35 Dihedral angle restraints: 14490 sinusoidal: 5782 harmonic: 8708 Sorted by residual: dihedral pdb=" CA HIS F 175 " pdb=" C HIS F 175 " pdb=" N PRO F 176 " pdb=" CA PRO F 176 " ideal model delta harmonic sigma weight residual 180.00 152.28 27.72 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA HIS B 175 " pdb=" C HIS B 175 " pdb=" N PRO B 176 " pdb=" CA PRO B 176 " ideal model delta harmonic sigma weight residual 180.00 152.29 27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA HIS C 175 " pdb=" C HIS C 175 " pdb=" N PRO C 176 " pdb=" CA PRO C 176 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 14487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2260 0.031 - 0.062: 1099 0.062 - 0.093: 299 0.093 - 0.124: 87 0.124 - 0.155: 21 Chirality restraints: 3766 Sorted by residual: chirality pdb=" CA ARG F 428 " pdb=" N ARG F 428 " pdb=" C ARG F 428 " pdb=" CB ARG F 428 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA ARG C 428 " pdb=" N ARG C 428 " pdb=" C ARG C 428 " pdb=" CB ARG C 428 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ARG E 428 " pdb=" N ARG E 428 " pdb=" C ARG E 428 " pdb=" CB ARG E 428 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 3763 not shown) Planarity restraints: 4046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 321 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 320 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO E 321 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 321 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 321 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 320 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO C 321 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 321 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 321 " 0.029 5.00e-02 4.00e+02 ... (remaining 4043 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1258 2.74 - 3.28: 24943 3.28 - 3.82: 36881 3.82 - 4.36: 42984 4.36 - 4.90: 73983 Nonbonded interactions: 180049 Sorted by model distance: nonbonded pdb=" O SER C 433 " pdb=" OG SER D 433 " model vdw 2.194 2.440 nonbonded pdb=" O GLU E 196 " pdb=" OG SER F 393 " model vdw 2.229 2.440 nonbonded pdb=" OG SER G 348 " pdb=" OE1 GLU G 349 " model vdw 2.255 2.440 nonbonded pdb=" OG SER B 348 " pdb=" OE1 GLU B 349 " model vdw 2.256 2.440 nonbonded pdb=" OG SER A 348 " pdb=" OE1 GLU A 349 " model vdw 2.256 2.440 ... (remaining 180044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.090 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 60.200 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 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 : 0.003 0.044 23989 Z= 0.171 Angle : 0.622 7.285 32529 Z= 0.318 Chirality : 0.040 0.155 3766 Planarity : 0.004 0.051 4046 Dihedral : 14.172 83.002 8792 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.03 % Favored : 88.73 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 2919 helix: 0.34 (0.14), residues: 1414 sheet: 1.23 (0.44), residues: 84 loop : -3.37 (0.15), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 127 HIS 0.003 0.001 HIS F 5 PHE 0.015 0.001 PHE G 307 TYR 0.007 0.001 TYR G 121 ARG 0.004 0.000 ARG E 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8093 (mm) cc_final: 0.7724 (mm) REVERT: A 344 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7446 (mt-10) REVERT: B 52 LEU cc_start: 0.8058 (mm) cc_final: 0.7698 (mm) REVERT: B 134 HIS cc_start: 0.7785 (m90) cc_final: 0.7509 (m-70) REVERT: B 351 LYS cc_start: 0.8052 (mppt) cc_final: 0.7684 (mmmt) REVERT: B 360 GLU cc_start: 0.7536 (pm20) cc_final: 0.7315 (pm20) REVERT: B 392 MET cc_start: 0.4481 (pmm) cc_final: 0.3232 (pmm) REVERT: C 360 GLU cc_start: 0.7512 (pm20) cc_final: 0.6869 (pm20) REVERT: C 392 MET cc_start: 0.4383 (pmm) cc_final: 0.3720 (tmm) REVERT: D 351 LYS cc_start: 0.7976 (mppt) cc_final: 0.7376 (mptt) REVERT: D 360 GLU cc_start: 0.7395 (pm20) cc_final: 0.7067 (pm20) REVERT: D 392 MET cc_start: 0.4353 (pmm) cc_final: 0.3352 (pmm) REVERT: E 52 LEU cc_start: 0.8205 (mm) cc_final: 0.7777 (mm) REVERT: E 349 GLU cc_start: 0.7458 (pm20) cc_final: 0.7250 (pm20) REVERT: E 351 LYS cc_start: 0.8048 (mppt) cc_final: 0.7462 (mptt) REVERT: E 360 GLU cc_start: 0.7504 (pm20) cc_final: 0.7240 (pm20) REVERT: E 392 MET cc_start: 0.4590 (pmm) cc_final: 0.3420 (pmm) REVERT: F 52 LEU cc_start: 0.8154 (mm) cc_final: 0.7733 (mm) REVERT: F 134 HIS cc_start: 0.7843 (m90) cc_final: 0.7584 (m-70) REVERT: G 52 LEU cc_start: 0.8042 (mm) cc_final: 0.7704 (mm) REVERT: G 351 LYS cc_start: 0.8048 (mppt) cc_final: 0.7584 (mmmt) REVERT: G 360 GLU cc_start: 0.7540 (pm20) cc_final: 0.7282 (pm20) REVERT: G 392 MET cc_start: 0.5018 (pmm) cc_final: 0.3600 (pmm) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.3504 time to fit residues: 177.9075 Evaluate side-chains 204 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 0.0070 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 119 optimal weight: 40.0000 chunk 230 optimal weight: 2.9990 chunk 89 optimal weight: 0.0010 chunk 140 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 266 optimal weight: 7.9990 overall best weight: 1.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN C 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23989 Z= 0.201 Angle : 0.662 6.002 32529 Z= 0.342 Chirality : 0.041 0.155 3766 Planarity : 0.005 0.047 4046 Dihedral : 6.285 78.918 3143 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.65 % Favored : 89.11 % Rotamer: Outliers : 0.87 % Allowed : 7.48 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.16), residues: 2919 helix: 0.86 (0.15), residues: 1400 sheet: 2.32 (0.37), residues: 42 loop : -3.31 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 74 HIS 0.004 0.001 HIS D 5 PHE 0.017 0.001 PHE A 307 TYR 0.019 0.001 TYR C 121 ARG 0.006 0.001 ARG G 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 263 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7144 (tt) REVERT: B 360 GLU cc_start: 0.7427 (pm20) cc_final: 0.7152 (pm20) REVERT: C 351 LYS cc_start: 0.8386 (mmtm) cc_final: 0.7392 (mptt) REVERT: C 360 GLU cc_start: 0.7478 (pm20) cc_final: 0.7235 (pm20) REVERT: C 392 MET cc_start: 0.4425 (pmm) cc_final: 0.3155 (tmm) REVERT: E 345 GLU cc_start: 0.7848 (tp30) cc_final: 0.7387 (tp30) REVERT: E 351 LYS cc_start: 0.7862 (mppt) cc_final: 0.7283 (mptt) REVERT: E 360 GLU cc_start: 0.7437 (pm20) cc_final: 0.7196 (pm20) outliers start: 23 outliers final: 11 residues processed: 272 average time/residue: 0.3189 time to fit residues: 140.8495 Evaluate side-chains 226 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 214 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 222 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 73 optimal weight: 0.0570 chunk 267 optimal weight: 50.0000 chunk 288 optimal weight: 20.0000 chunk 238 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23989 Z= 0.217 Angle : 0.625 6.165 32529 Z= 0.323 Chirality : 0.041 0.150 3766 Planarity : 0.005 0.053 4046 Dihedral : 6.234 77.122 3143 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.55 % Favored : 88.22 % Rotamer: Outliers : 2.13 % Allowed : 12.23 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.16), residues: 2919 helix: 0.86 (0.15), residues: 1400 sheet: 2.31 (0.34), residues: 42 loop : -3.37 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 74 HIS 0.003 0.001 HIS G 5 PHE 0.025 0.001 PHE B 307 TYR 0.015 0.001 TYR C 121 ARG 0.004 0.000 ARG E 428 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 228 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7187 (tt) REVERT: B 360 GLU cc_start: 0.7548 (pm20) cc_final: 0.7277 (pm20) REVERT: C 349 GLU cc_start: 0.7261 (pm20) cc_final: 0.7006 (pm20) REVERT: C 351 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7422 (mptt) REVERT: C 360 GLU cc_start: 0.7547 (pm20) cc_final: 0.7253 (pm20) REVERT: E 128 ARG cc_start: 0.7992 (tmm-80) cc_final: 0.7694 (ttt180) REVERT: E 345 GLU cc_start: 0.7721 (tp30) cc_final: 0.7340 (tp30) REVERT: E 360 GLU cc_start: 0.7595 (pm20) cc_final: 0.7362 (pm20) REVERT: F 344 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6912 (tt0) REVERT: G 351 LYS cc_start: 0.8338 (mmtm) cc_final: 0.7610 (mptt) outliers start: 56 outliers final: 39 residues processed: 256 average time/residue: 0.3262 time to fit residues: 135.0286 Evaluate side-chains 249 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 209 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 303 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 chunk 268 optimal weight: 50.0000 chunk 284 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 76 optimal weight: 0.0170 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN B 282 GLN C 282 GLN C 403 GLN D 282 GLN E 282 GLN F 282 GLN G 282 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23989 Z= 0.174 Angle : 0.600 7.224 32529 Z= 0.307 Chirality : 0.040 0.145 3766 Planarity : 0.005 0.052 4046 Dihedral : 6.098 74.234 3143 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.83 % Favored : 88.93 % Rotamer: Outliers : 1.67 % Allowed : 14.10 % Favored : 84.23 % 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: -1.55 (0.16), residues: 2919 helix: 1.01 (0.15), residues: 1386 sheet: 2.36 (0.36), residues: 42 loop : -3.37 (0.14), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 74 HIS 0.002 0.000 HIS G 5 PHE 0.018 0.001 PHE B 307 TYR 0.012 0.001 TYR A 221 ARG 0.003 0.000 ARG E 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 236 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LYS cc_start: 0.8390 (mmtm) cc_final: 0.7610 (mptt) REVERT: B 351 LYS cc_start: 0.8520 (mptt) cc_final: 0.7882 (mptt) REVERT: C 349 GLU cc_start: 0.7396 (pm20) cc_final: 0.7065 (pm20) REVERT: C 351 LYS cc_start: 0.8332 (mmtm) cc_final: 0.7619 (mptt) REVERT: C 360 GLU cc_start: 0.7573 (pm20) cc_final: 0.7276 (pm20) REVERT: E 128 ARG cc_start: 0.8015 (tmm-80) cc_final: 0.7695 (ttt180) REVERT: E 344 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7239 (tt0) REVERT: E 351 LYS cc_start: 0.8266 (mmtm) cc_final: 0.7453 (mptt) REVERT: F 344 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6934 (tt0) REVERT: G 351 LYS cc_start: 0.8154 (mmtm) cc_final: 0.7503 (mmmt) outliers start: 44 outliers final: 36 residues processed: 252 average time/residue: 0.3209 time to fit residues: 129.3070 Evaluate side-chains 256 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 220 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 345 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 0.7980 chunk 161 optimal weight: 40.0000 chunk 4 optimal weight: 5.9990 chunk 211 optimal weight: 0.3980 chunk 117 optimal weight: 8.9990 chunk 242 optimal weight: 8.9990 chunk 196 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 255 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 overall best weight: 4.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN B 76 GLN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN D 76 GLN D 206 GLN ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 206 GLN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN F 206 GLN ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN G 206 GLN ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 23989 Z= 0.401 Angle : 0.766 6.682 32529 Z= 0.399 Chirality : 0.046 0.146 3766 Planarity : 0.005 0.055 4046 Dihedral : 6.396 70.703 3143 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.13 % Favored : 87.63 % Rotamer: Outliers : 3.12 % Allowed : 14.97 % Favored : 81.91 % 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: -2.12 (0.16), residues: 2919 helix: 0.36 (0.14), residues: 1393 sheet: -0.37 (0.39), residues: 126 loop : -3.57 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 104 HIS 0.007 0.001 HIS B 5 PHE 0.050 0.003 PHE A 307 TYR 0.019 0.002 TYR A 121 ARG 0.009 0.001 ARG E 426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 232 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6978 (t70) REVERT: A 128 ARG cc_start: 0.7961 (tmm-80) cc_final: 0.7591 (ttt180) REVERT: A 351 LYS cc_start: 0.8486 (mmtm) cc_final: 0.7674 (mptt) REVERT: A 410 MET cc_start: 0.4618 (mpp) cc_final: 0.4413 (mpp) REVERT: C 351 LYS cc_start: 0.8602 (mmtm) cc_final: 0.7939 (mptt) REVERT: C 360 GLU cc_start: 0.7903 (pm20) cc_final: 0.7630 (pm20) REVERT: D 128 ARG cc_start: 0.8013 (tmm-80) cc_final: 0.7691 (ttt180) REVERT: D 206 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7329 (mm-40) REVERT: D 345 GLU cc_start: 0.7967 (tp30) cc_final: 0.7609 (tp30) REVERT: E 128 ARG cc_start: 0.8019 (tmm-80) cc_final: 0.7713 (ttt180) REVERT: E 340 ASN cc_start: 0.7619 (m110) cc_final: 0.6985 (t0) REVERT: E 344 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7139 (tt0) REVERT: E 345 GLU cc_start: 0.7922 (tp30) cc_final: 0.7566 (tp30) REVERT: E 351 LYS cc_start: 0.8460 (mmtm) cc_final: 0.7699 (mptt) REVERT: F 344 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6886 (tt0) REVERT: G 128 ARG cc_start: 0.7822 (ttp-170) cc_final: 0.7535 (ttt180) REVERT: G 349 GLU cc_start: 0.7826 (pm20) cc_final: 0.7585 (pm20) REVERT: G 351 LYS cc_start: 0.8566 (mmtm) cc_final: 0.7861 (mptt) outliers start: 82 outliers final: 56 residues processed: 283 average time/residue: 0.3320 time to fit residues: 151.9159 Evaluate side-chains 250 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 192 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 305 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 166 optimal weight: 50.0000 chunk 70 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 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 282 GLN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN C 76 GLN ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 23989 Z= 0.290 Angle : 0.684 7.825 32529 Z= 0.355 Chirality : 0.044 0.214 3766 Planarity : 0.005 0.054 4046 Dihedral : 6.336 68.674 3143 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.55 % Favored : 88.22 % Rotamer: Outliers : 3.27 % Allowed : 16.19 % Favored : 80.55 % 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: -2.02 (0.16), residues: 2919 helix: 0.51 (0.15), residues: 1393 sheet: -0.44 (0.39), residues: 126 loop : -3.58 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 104 HIS 0.005 0.001 HIS G 5 PHE 0.025 0.002 PHE C 307 TYR 0.014 0.002 TYR A 221 ARG 0.005 0.001 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 222 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6873 (t70) REVERT: A 128 ARG cc_start: 0.8090 (tmm-80) cc_final: 0.7671 (ttt180) REVERT: A 318 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6698 (pp20) REVERT: A 351 LYS cc_start: 0.8437 (mmtm) cc_final: 0.7604 (mptt) REVERT: A 410 MET cc_start: 0.4739 (mpp) cc_final: 0.4535 (mpp) REVERT: C 318 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6577 (pp20) REVERT: C 349 GLU cc_start: 0.7654 (pm20) cc_final: 0.7384 (pm20) REVERT: C 351 LYS cc_start: 0.8632 (mmtm) cc_final: 0.7919 (mptt) REVERT: C 360 GLU cc_start: 0.7945 (pm20) cc_final: 0.7683 (pm20) REVERT: D 128 ARG cc_start: 0.7980 (tmm-80) cc_final: 0.7604 (ttt180) REVERT: D 345 GLU cc_start: 0.7970 (tp30) cc_final: 0.7647 (tp30) REVERT: E 128 ARG cc_start: 0.8042 (tmm-80) cc_final: 0.7648 (ttt180) REVERT: E 340 ASN cc_start: 0.7563 (m110) cc_final: 0.6938 (t0) REVERT: E 344 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7119 (tt0) REVERT: E 345 GLU cc_start: 0.7990 (tp30) cc_final: 0.7629 (tp30) REVERT: E 351 LYS cc_start: 0.8450 (mmtm) cc_final: 0.8216 (mmtm) REVERT: F 344 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7057 (tt0) REVERT: G 128 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7305 (ttt180) REVERT: G 312 ASP cc_start: 0.5915 (OUTLIER) cc_final: 0.5048 (p0) REVERT: G 349 GLU cc_start: 0.7751 (pm20) cc_final: 0.7527 (pm20) REVERT: G 351 LYS cc_start: 0.8552 (mmtm) cc_final: 0.7790 (mptt) outliers start: 86 outliers final: 66 residues processed: 273 average time/residue: 0.3351 time to fit residues: 146.5383 Evaluate side-chains 271 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 201 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 312 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 283 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23989 Z= 0.196 Angle : 0.640 14.268 32529 Z= 0.327 Chirality : 0.042 0.634 3766 Planarity : 0.005 0.054 4046 Dihedral : 6.114 65.951 3143 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.33 % Favored : 87.43 % Rotamer: Outliers : 2.20 % Allowed : 17.93 % Favored : 79.86 % 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: -1.89 (0.16), residues: 2919 helix: 0.60 (0.15), residues: 1414 sheet: 0.48 (0.48), residues: 84 loop : -3.54 (0.14), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.004 0.000 HIS G 5 PHE 0.018 0.001 PHE C 307 TYR 0.014 0.001 TYR A 221 ARG 0.005 0.001 ARG F 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 233 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.8152 (tmm-80) cc_final: 0.7741 (ttt180) REVERT: A 318 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6564 (pp20) REVERT: A 351 LYS cc_start: 0.8349 (mmtm) cc_final: 0.7483 (mptt) REVERT: A 410 MET cc_start: 0.4727 (mpp) cc_final: 0.4432 (mpp) REVERT: B 318 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6525 (pp20) REVERT: C 318 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6426 (pp20) REVERT: C 351 LYS cc_start: 0.8440 (mmtm) cc_final: 0.7780 (mptt) REVERT: D 128 ARG cc_start: 0.7959 (tmm-80) cc_final: 0.7525 (ttt180) REVERT: D 345 GLU cc_start: 0.7917 (tp30) cc_final: 0.7630 (tp30) REVERT: E 128 ARG cc_start: 0.8092 (tmm-80) cc_final: 0.7692 (ttt180) REVERT: E 344 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7107 (tt0) REVERT: E 345 GLU cc_start: 0.8002 (tp30) cc_final: 0.7637 (tp30) REVERT: E 351 LYS cc_start: 0.8349 (mmtm) cc_final: 0.8116 (mmtm) REVERT: F 344 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7061 (tt0) REVERT: F 349 GLU cc_start: 0.7419 (pt0) cc_final: 0.7062 (pt0) REVERT: G 128 ARG cc_start: 0.7668 (ttp-170) cc_final: 0.7290 (ttt180) REVERT: G 318 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6693 (pp20) REVERT: G 351 LYS cc_start: 0.8399 (mmtm) cc_final: 0.7705 (mptt) outliers start: 58 outliers final: 48 residues processed: 261 average time/residue: 0.3341 time to fit residues: 138.6874 Evaluate side-chains 267 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 215 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 312 ASP Chi-restraints excluded: chain G residue 318 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 2.9990 chunk 113 optimal weight: 0.0000 chunk 169 optimal weight: 9.9990 chunk 85 optimal weight: 0.0980 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 193 optimal weight: 0.0770 chunk 140 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 overall best weight: 0.8346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN F 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23989 Z= 0.173 Angle : 0.618 14.480 32529 Z= 0.314 Chirality : 0.040 0.178 3766 Planarity : 0.005 0.054 4046 Dihedral : 5.859 61.706 3143 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.27 % Favored : 88.49 % Rotamer: Outliers : 1.98 % Allowed : 18.58 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2919 helix: 0.92 (0.15), residues: 1379 sheet: 0.32 (0.47), residues: 84 loop : -3.44 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.003 0.000 HIS F 5 PHE 0.020 0.001 PHE C 307 TYR 0.012 0.001 TYR G 221 ARG 0.005 0.001 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 240 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6478 (pp20) REVERT: A 410 MET cc_start: 0.4625 (mpp) cc_final: 0.4352 (mpp) REVERT: B 318 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6224 (pp20) REVERT: C 349 GLU cc_start: 0.7577 (pm20) cc_final: 0.7280 (pm20) REVERT: C 351 LYS cc_start: 0.8204 (mmtm) cc_final: 0.7512 (mptt) REVERT: C 392 MET cc_start: 0.3773 (tmm) cc_final: 0.2711 (pmm) REVERT: D 128 ARG cc_start: 0.8017 (tmm-80) cc_final: 0.7589 (ttt180) REVERT: D 318 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6097 (tm-30) REVERT: D 345 GLU cc_start: 0.7945 (tp30) cc_final: 0.7668 (tp30) REVERT: E 128 ARG cc_start: 0.8127 (tmm-80) cc_final: 0.7711 (ttt180) REVERT: E 318 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6120 (tm-30) REVERT: E 344 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7088 (tt0) REVERT: E 351 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7947 (mmtm) REVERT: F 318 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6150 (pp20) REVERT: F 344 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7036 (tt0) REVERT: G 128 ARG cc_start: 0.7735 (ttp-170) cc_final: 0.7358 (ttt180) REVERT: G 318 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6489 (pp20) REVERT: G 349 GLU cc_start: 0.7574 (pm20) cc_final: 0.7367 (pm20) REVERT: G 351 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7454 (mptt) outliers start: 52 outliers final: 40 residues processed: 266 average time/residue: 0.3340 time to fit residues: 141.5106 Evaluate side-chains 271 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 225 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 318 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 10.0000 chunk 271 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 264 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 81 optimal weight: 0.0970 chunk 238 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23989 Z= 0.170 Angle : 0.613 14.270 32529 Z= 0.310 Chirality : 0.040 0.149 3766 Planarity : 0.005 0.064 4046 Dihedral : 5.708 57.772 3143 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.33 % Favored : 87.43 % Rotamer: Outliers : 1.56 % Allowed : 19.41 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2919 helix: 0.99 (0.15), residues: 1379 sheet: 0.23 (0.46), residues: 84 loop : -3.40 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 104 HIS 0.003 0.000 HIS F 5 PHE 0.013 0.001 PHE F 307 TYR 0.011 0.001 TYR A 221 ARG 0.012 0.001 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 236 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6283 (pp20) REVERT: A 351 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7563 (mptt) REVERT: A 410 MET cc_start: 0.4636 (mpp) cc_final: 0.4319 (mpp) REVERT: C 349 GLU cc_start: 0.7490 (pm20) cc_final: 0.7182 (pm20) REVERT: C 351 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7495 (mptt) REVERT: C 392 MET cc_start: 0.3767 (tmm) cc_final: 0.2685 (pmm) REVERT: D 318 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.5949 (tm-30) REVERT: D 345 GLU cc_start: 0.7898 (tp30) cc_final: 0.7627 (tp30) REVERT: D 392 MET cc_start: 0.3727 (pmm) cc_final: 0.3419 (tmm) REVERT: E 128 ARG cc_start: 0.8149 (tmm-80) cc_final: 0.7721 (ttt180) REVERT: E 318 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.5970 (tm-30) REVERT: E 344 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7083 (tt0) REVERT: E 351 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7923 (mmtm) REVERT: F 318 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5981 (pp20) REVERT: F 344 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7015 (tt0) REVERT: G 128 ARG cc_start: 0.7741 (ttp-170) cc_final: 0.7383 (ttt180) REVERT: G 318 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6341 (pp20) outliers start: 41 outliers final: 36 residues processed: 259 average time/residue: 0.3532 time to fit residues: 146.8877 Evaluate side-chains 269 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 228 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 318 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 3.9990 chunk 279 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 292 optimal weight: 50.0000 chunk 269 optimal weight: 50.0000 chunk 233 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 143 optimal weight: 50.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23989 Z= 0.185 Angle : 0.619 13.991 32529 Z= 0.313 Chirality : 0.040 0.157 3766 Planarity : 0.005 0.054 4046 Dihedral : 5.610 53.620 3143 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.92 % Favored : 87.84 % Rotamer: Outliers : 1.79 % Allowed : 19.38 % Favored : 78.84 % 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: -1.57 (0.16), residues: 2919 helix: 1.00 (0.15), residues: 1379 sheet: 0.26 (0.46), residues: 84 loop : -3.40 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.003 0.000 HIS F 5 PHE 0.015 0.001 PHE E 307 TYR 0.011 0.001 TYR D 221 ARG 0.005 0.001 ARG F 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 231 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6106 (pp20) REVERT: A 351 LYS cc_start: 0.8295 (mmtm) cc_final: 0.7557 (mptt) REVERT: A 410 MET cc_start: 0.4693 (mpp) cc_final: 0.4392 (mpp) REVERT: B 318 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5999 (pp20) REVERT: C 318 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6344 (pp20) REVERT: C 349 GLU cc_start: 0.7464 (pm20) cc_final: 0.7141 (pm20) REVERT: C 351 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7511 (mptt) REVERT: C 360 GLU cc_start: 0.7989 (pm20) cc_final: 0.7730 (pm20) REVERT: C 392 MET cc_start: 0.3800 (tmm) cc_final: 0.2701 (pmm) REVERT: D 128 ARG cc_start: 0.8053 (tmm-80) cc_final: 0.7685 (ttt180) REVERT: D 318 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.5968 (tm-30) REVERT: D 345 GLU cc_start: 0.7917 (tp30) cc_final: 0.7627 (tp30) REVERT: D 392 MET cc_start: 0.3640 (pmm) cc_final: 0.3332 (tmm) REVERT: E 128 ARG cc_start: 0.8160 (tmm-80) cc_final: 0.7733 (ttt180) REVERT: E 318 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6070 (pp20) REVERT: E 344 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7128 (tt0) REVERT: E 351 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7964 (mmtm) REVERT: F 318 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6063 (pp20) REVERT: F 344 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7025 (tt0) REVERT: F 351 LYS cc_start: 0.8415 (mmtm) cc_final: 0.7632 (mmtt) REVERT: G 128 ARG cc_start: 0.7861 (ttp-170) cc_final: 0.7524 (ttt180) REVERT: G 318 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6264 (pp20) REVERT: G 351 LYS cc_start: 0.8455 (mmtm) cc_final: 0.7819 (mmmt) outliers start: 47 outliers final: 36 residues processed: 260 average time/residue: 0.3387 time to fit residues: 139.3513 Evaluate side-chains 269 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 345 GLU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 318 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 50.0000 chunk 248 optimal weight: 30.0000 chunk 71 optimal weight: 0.0050 chunk 215 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 29 optimal weight: 0.0040 chunk 43 optimal weight: 0.0170 overall best weight: 0.9446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN B 282 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN G 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.228155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.152908 restraints weight = 28417.497| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.40 r_work: 0.3660 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23989 Z= 0.173 Angle : 0.614 13.898 32529 Z= 0.310 Chirality : 0.040 0.144 3766 Planarity : 0.005 0.054 4046 Dihedral : 5.511 49.613 3143 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.78 % Favored : 87.98 % Rotamer: Outliers : 1.71 % Allowed : 19.68 % Favored : 78.61 % 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: -1.53 (0.16), residues: 2919 helix: 1.04 (0.15), residues: 1379 sheet: 0.21 (0.46), residues: 84 loop : -3.39 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.003 0.000 HIS C 5 PHE 0.016 0.001 PHE C 307 TYR 0.011 0.001 TYR A 221 ARG 0.005 0.001 ARG B 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4662.25 seconds wall clock time: 86 minutes 34.62 seconds (5194.62 seconds total)