Starting phenix.real_space_refine on Thu Aug 8 13:01:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwb_30880/08_2024/7dwb_30880.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwb_30880/08_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_30880/08_2024/7dwb_30880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwb_30880/08_2024/7dwb_30880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwb_30880/08_2024/7dwb_30880.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwb_30880/08_2024/7dwb_30880.cif" } 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-5409/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: 11.92, per 1000 atoms: 0.51 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: 8.82 Conformation dependent library (CDL) restraints added in 4.0 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: 1.98 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: 5.86 Time building geometry restraints manager: 9.75 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 3.040 nonbonded pdb=" O GLU E 196 " pdb=" OG SER F 393 " model vdw 2.229 3.040 nonbonded pdb=" OG SER G 348 " pdb=" OE1 GLU G 349 " model vdw 2.255 3.040 nonbonded pdb=" OG SER B 348 " pdb=" OE1 GLU B 349 " model vdw 2.256 3.040 nonbonded pdb=" OG SER A 348 " pdb=" OE1 GLU A 349 " model vdw 2.256 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 55.830 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.960 ------------------------------------------------------------------------------- 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 : 2.347 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: 0.3635 time to fit residues: 184.1922 Evaluate side-chains 204 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.256 ------------------------------------------------------------------------------- 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: 3.9990 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 30.0000 chunk 230 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.7186 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23989 Z= 0.230 Angle : 0.678 5.833 32529 Z= 0.352 Chirality : 0.043 0.149 3766 Planarity : 0.005 0.048 4046 Dihedral : 6.401 82.103 3143 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.00 % Favored : 89.76 % Rotamer: Outliers : 1.33 % Allowed : 7.71 % Favored : 90.96 % 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: -1.73 (0.16), residues: 2919 helix: 0.65 (0.15), residues: 1442 sheet: None (None), residues: 0 loop : -3.20 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.004 0.001 HIS F 106 PHE 0.021 0.001 PHE G 307 TYR 0.020 0.002 TYR A 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 288 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 253 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 351 LYS cc_start: 0.8415 (mmtm) cc_final: 0.7461 (mptt) REVERT: E 345 GLU cc_start: 0.7745 (tp30) cc_final: 0.7297 (tp30) REVERT: E 351 LYS cc_start: 0.7883 (mppt) cc_final: 0.7349 (mptt) REVERT: G 344 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7054 (mt-10) outliers start: 35 outliers final: 21 residues processed: 265 average time/residue: 0.3256 time to fit residues: 140.1328 Evaluate side-chains 235 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 214 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain G residue 48 LEU 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 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 222 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 73 optimal weight: 0.0270 chunk 267 optimal weight: 9.9990 chunk 288 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- 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 G 282 GLN G 403 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2112 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= 0.214 Angle : 0.640 6.166 32529 Z= 0.330 Chirality : 0.041 0.147 3766 Planarity : 0.005 0.054 4046 Dihedral : 6.369 81.413 3143 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.35 % Favored : 89.41 % Rotamer: Outliers : 1.90 % Allowed : 12.12 % Favored : 85.98 % 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: -1.68 (0.16), residues: 2919 helix: 0.73 (0.15), residues: 1407 sheet: 0.78 (0.46), residues: 84 loop : -3.36 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 74 HIS 0.003 0.001 HIS F 5 PHE 0.022 0.001 PHE B 307 TYR 0.014 0.001 TYR C 121 ARG 0.004 0.001 ARG F 225 *********************** 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 273 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 223 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 351 LYS cc_start: 0.8457 (mmtm) cc_final: 0.7698 (mptt) REVERT: E 345 GLU cc_start: 0.7830 (tp30) cc_final: 0.7457 (tp30) REVERT: F 344 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6879 (tt0) REVERT: G 344 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7135 (tt0) REVERT: G 351 LYS cc_start: 0.8328 (mmtm) cc_final: 0.7646 (mptt) outliers start: 50 outliers final: 35 residues processed: 247 average time/residue: 0.3603 time to fit residues: 144.7204 Evaluate side-chains 237 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 2.652 ------------------------------------------------------------------------------- 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 B residue 40 CYS Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 222 ILE 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 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 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 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: 6.9990 chunk 138 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 chunk 127 optimal weight: 0.0570 chunk 179 optimal weight: 3.9990 chunk 268 optimal weight: 40.0000 chunk 284 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23989 Z= 0.211 Angle : 0.639 6.849 32529 Z= 0.327 Chirality : 0.041 0.142 3766 Planarity : 0.005 0.052 4046 Dihedral : 6.341 80.845 3143 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.69 % Favored : 89.07 % Rotamer: Outliers : 1.86 % Allowed : 13.56 % Favored : 84.57 % 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: -1.75 (0.16), residues: 2919 helix: 0.68 (0.15), residues: 1407 sheet: 0.70 (0.45), residues: 84 loop : -3.41 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 104 HIS 0.003 0.001 HIS G 5 PHE 0.025 0.001 PHE E 307 TYR 0.013 0.001 TYR A 221 ARG 0.004 0.001 ARG F 225 *********************** 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 267 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 218 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LYS cc_start: 0.8453 (mmtm) cc_final: 0.7760 (mptt) REVERT: C 351 LYS cc_start: 0.8488 (mmtm) cc_final: 0.7788 (mptt) REVERT: E 351 LYS cc_start: 0.8302 (mmtm) cc_final: 0.7462 (mptt) REVERT: F 344 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6965 (tt0) REVERT: G 344 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7182 (tt0) REVERT: G 351 LYS cc_start: 0.8336 (mmtm) cc_final: 0.7570 (mptt) outliers start: 49 outliers final: 41 residues processed: 240 average time/residue: 0.3286 time to fit residues: 128.1420 Evaluate side-chains 243 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 202 time to evaluate : 2.366 ------------------------------------------------------------------------------- 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 B residue 40 CYS 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 345 GLU Chi-restraints excluded: chain C residue 48 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 345 GLU Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 143 MET 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 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 290 VAL Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 303 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 2.9990 chunk 161 optimal weight: 30.0000 chunk 4 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 117 optimal weight: 0.0170 chunk 242 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 0.1980 chunk 255 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.6424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23989 Z= 0.252 Angle : 0.669 7.186 32529 Z= 0.342 Chirality : 0.042 0.141 3766 Planarity : 0.005 0.056 4046 Dihedral : 6.353 79.234 3143 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.17 % Favored : 88.59 % Rotamer: Outliers : 3.15 % Allowed : 13.98 % Favored : 82.86 % 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: -1.82 (0.16), residues: 2919 helix: 0.65 (0.15), residues: 1393 sheet: 0.70 (0.45), residues: 84 loop : -3.44 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 104 HIS 0.004 0.001 HIS G 5 PHE 0.032 0.002 PHE A 307 TYR 0.016 0.002 TYR G 221 ARG 0.006 0.001 ARG F 225 *********************** 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 312 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 229 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LYS cc_start: 0.8447 (mmtm) cc_final: 0.7685 (mptt) REVERT: B 128 ARG cc_start: 0.7879 (ttp-170) cc_final: 0.7520 (ttt180) REVERT: B 349 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: C 351 LYS cc_start: 0.8507 (mmtm) cc_final: 0.7786 (mptt) REVERT: D 345 GLU cc_start: 0.7887 (tp30) cc_final: 0.7556 (tp30) REVERT: E 351 LYS cc_start: 0.8337 (mmtm) cc_final: 0.7419 (mptt) REVERT: F 344 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6933 (tt0) REVERT: G 128 ARG cc_start: 0.7694 (ttp-170) cc_final: 0.7398 (ttt180) REVERT: G 344 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: G 351 LYS cc_start: 0.8415 (mmtm) cc_final: 0.7645 (mptt) outliers start: 83 outliers final: 57 residues processed: 277 average time/residue: 0.3145 time to fit residues: 140.9940 Evaluate side-chains 272 residues out of total 2639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 213 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU 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 290 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 40 CYS 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 B residue 349 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 52 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 345 GLU 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 143 MET 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 D residue 305 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 139 LEU 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 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 233 LEU 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 F residue 429 LEU 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 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 Chi-restraints excluded: chain G residue 344 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 73.4603 > 50: distance: 19 - 45: 24.233 distance: 26 - 31: 35.255 distance: 27 - 53: 36.724 distance: 31 - 32: 40.548 distance: 32 - 33: 36.173 distance: 32 - 35: 17.444 distance: 33 - 34: 19.532 distance: 33 - 38: 52.596 distance: 34 - 64: 59.434 distance: 35 - 36: 21.461 distance: 36 - 37: 56.847 distance: 38 - 39: 40.462 distance: 38 - 44: 38.805 distance: 39 - 40: 56.683 distance: 40 - 41: 31.165 distance: 40 - 45: 40.335 distance: 41 - 78: 3.298 distance: 43 - 44: 56.366 distance: 45 - 46: 30.162 distance: 46 - 47: 3.506 distance: 46 - 49: 55.134 distance: 48 - 89: 40.555 distance: 49 - 50: 6.385 distance: 50 - 51: 53.294 distance: 50 - 52: 50.929 distance: 54 - 55: 56.358 distance: 55 - 56: 41.066 distance: 55 - 64: 39.065 distance: 56 - 100: 65.696 distance: 57 - 58: 41.064 distance: 58 - 59: 26.273 distance: 58 - 60: 28.525 distance: 60 - 62: 40.911 distance: 61 - 63: 40.248 distance: 65 - 66: 57.184 distance: 65 - 68: 40.101 distance: 66 - 78: 39.525 distance: 67 - 105: 72.693 distance: 68 - 69: 40.850 distance: 69 - 70: 41.835 distance: 69 - 71: 56.622 distance: 70 - 72: 16.972 distance: 71 - 73: 22.468 distance: 71 - 74: 21.779 distance: 72 - 73: 17.879 distance: 74 - 76: 44.641 distance: 75 - 77: 45.075 distance: 76 - 77: 20.766 distance: 78 - 79: 40.450 distance: 82 - 83: 55.476 distance: 85 - 86: 23.970 distance: 86 - 87: 40.858 distance: 86 - 88: 23.205 distance: 89 - 90: 39.590 distance: 90 - 91: 41.182 distance: 91 - 100: 40.157 distance: 93 - 94: 32.187 distance: 94 - 95: 5.561 distance: 94 - 96: 7.075 distance: 95 - 97: 39.466 distance: 96 - 98: 41.040 distance: 97 - 99: 38.724 distance: 98 - 99: 40.653 distance: 100 - 101: 6.658 distance: 101 - 102: 57.741 distance: 101 - 104: 39.305 distance: 102 - 105: 56.671 distance: 105 - 106: 57.317 distance: 106 - 107: 40.328 distance: 106 - 109: 39.411 distance: 107 - 108: 40.465 distance: 107 - 110: 40.382 distance: 111 - 112: 38.668 distance: 111 - 114: 57.922 distance: 112 - 113: 57.410 distance: 112 - 115: 35.504 distance: 113 - 135: 32.926 distance: 155 - 159: 3.016