Starting phenix.real_space_refine on Sat Feb 17 01:00:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz7_29605/02_2024/8fz7_29605_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz7_29605/02_2024/8fz7_29605.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz7_29605/02_2024/8fz7_29605_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz7_29605/02_2024/8fz7_29605_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz7_29605/02_2024/8fz7_29605_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz7_29605/02_2024/8fz7_29605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz7_29605/02_2024/8fz7_29605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz7_29605/02_2024/8fz7_29605_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fz7_29605/02_2024/8fz7_29605_updated.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 68 5.16 5 C 10728 2.51 5 N 2897 2.21 5 O 3272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 16971 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2473 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2473 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "E" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2473 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "G" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2473 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "D" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "F" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' K': 2, 'PGW': 1, 'YQ1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.35, per 1000 atoms: 0.55 Number of scatterers: 16971 At special positions: 0 Unit cell: (150.481, 150.481, 118.003, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 68 16.00 P 4 15.00 O 3272 8.00 N 2897 7.00 C 10728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.55 Conformation dependent library (CDL) restraints added in 3.2 seconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 16 sheets defined 45.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 22 through 42 Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 70 through 107 removed outlier: 3.760A pdb=" N MET A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.511A pdb=" N LEU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 removed outlier: 4.114A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.569A pdb=" N LYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 201 removed outlier: 3.545A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 removed outlier: 4.392A pdb=" N GLU A 218 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 280 through 283 No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 285 through 288 No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.694A pdb=" N GLU A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 42 Processing helix chain 'C' and resid 46 through 57 Processing helix chain 'C' and resid 70 through 107 removed outlier: 3.761A pdb=" N MET C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 133 removed outlier: 3.512A pdb=" N LEU C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 removed outlier: 4.114A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 151 " --> pdb=" O ASN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 removed outlier: 3.569A pdb=" N LYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 removed outlier: 3.544A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 223 removed outlier: 4.392A pdb=" N GLU C 218 " --> pdb=" O GLU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 280 through 283 No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 285 through 288 No H-bonds generated for 'chain 'C' and resid 285 through 288' Processing helix chain 'C' and resid 324 through 331 removed outlier: 3.693A pdb=" N GLU C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 42 Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 70 through 107 removed outlier: 3.761A pdb=" N MET E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 133 removed outlier: 3.512A pdb=" N LEU E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 155 removed outlier: 4.115A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 removed outlier: 3.569A pdb=" N LYS E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 201 removed outlier: 3.544A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 223 removed outlier: 4.391A pdb=" N GLU E 218 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 241 Processing helix chain 'E' and resid 247 through 255 Processing helix chain 'E' and resid 280 through 283 No H-bonds generated for 'chain 'E' and resid 280 through 283' Processing helix chain 'E' and resid 285 through 288 No H-bonds generated for 'chain 'E' and resid 285 through 288' Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.693A pdb=" N GLU E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG E 329 " --> pdb=" O GLU E 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 42 Processing helix chain 'G' and resid 46 through 57 Processing helix chain 'G' and resid 70 through 107 removed outlier: 3.760A pdb=" N MET G 107 " --> pdb=" O GLN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 133 removed outlier: 3.512A pdb=" N LEU G 131 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG G 132 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU G 133 " --> pdb=" O GLU G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 155 removed outlier: 4.114A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 172 removed outlier: 3.569A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 201 removed outlier: 3.546A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 223 removed outlier: 4.392A pdb=" N GLU G 218 " --> pdb=" O GLU G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 241 Processing helix chain 'G' and resid 247 through 255 Processing helix chain 'G' and resid 280 through 283 No H-bonds generated for 'chain 'G' and resid 280 through 283' Processing helix chain 'G' and resid 285 through 288 No H-bonds generated for 'chain 'G' and resid 285 through 288' Processing helix chain 'G' and resid 324 through 331 removed outlier: 3.693A pdb=" N GLU G 328 " --> pdb=" O PRO G 324 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 removed outlier: 3.568A pdb=" N ARG B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 155 removed outlier: 4.062A pdb=" N LYS B 150 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.612A pdb=" N LYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 201 Processing helix chain 'B' and resid 214 through 223 removed outlier: 4.488A pdb=" N GLU B 218 " --> pdb=" O GLU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 280 through 283 No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 285 through 289 Processing helix chain 'B' and resid 324 through 333 removed outlier: 3.607A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 133 removed outlier: 3.568A pdb=" N ARG D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 155 removed outlier: 4.062A pdb=" N LYS D 150 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 removed outlier: 3.613A pdb=" N LYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 214 through 223 removed outlier: 4.488A pdb=" N GLU D 218 " --> pdb=" O GLU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 248 through 255 Processing helix chain 'D' and resid 280 through 283 No H-bonds generated for 'chain 'D' and resid 280 through 283' Processing helix chain 'D' and resid 285 through 289 Processing helix chain 'D' and resid 324 through 333 removed outlier: 3.607A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 133 removed outlier: 3.568A pdb=" N ARG F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU F 133 " --> pdb=" O GLU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 155 removed outlier: 4.062A pdb=" N LYS F 150 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 removed outlier: 3.613A pdb=" N LYS F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 201 Processing helix chain 'F' and resid 214 through 223 removed outlier: 4.487A pdb=" N GLU F 218 " --> pdb=" O GLU F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 241 Processing helix chain 'F' and resid 248 through 255 Processing helix chain 'F' and resid 280 through 283 No H-bonds generated for 'chain 'F' and resid 280 through 283' Processing helix chain 'F' and resid 285 through 289 Processing helix chain 'F' and resid 324 through 333 removed outlier: 3.608A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 133 removed outlier: 3.568A pdb=" N ARG H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU H 133 " --> pdb=" O GLU H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 155 removed outlier: 4.063A pdb=" N LYS H 150 " --> pdb=" O ASN H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 172 removed outlier: 3.612A pdb=" N LYS H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 201 Processing helix chain 'H' and resid 214 through 223 removed outlier: 4.488A pdb=" N GLU H 218 " --> pdb=" O GLU H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 241 Processing helix chain 'H' and resid 248 through 255 Processing helix chain 'H' and resid 280 through 283 No H-bonds generated for 'chain 'H' and resid 280 through 283' Processing helix chain 'H' and resid 285 through 289 Processing helix chain 'H' and resid 324 through 333 removed outlier: 3.607A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 227 through 229 removed outlier: 6.495A pdb=" N VAL A 181 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N GLU A 210 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL A 183 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN A 158 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA A 143 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 160 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.977A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 227 through 229 removed outlier: 6.494A pdb=" N VAL C 181 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N GLU C 210 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL C 183 " --> pdb=" O GLU C 210 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN C 158 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA C 143 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL C 160 " --> pdb=" O ALA C 143 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.977A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 227 through 229 removed outlier: 6.494A pdb=" N VAL E 181 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N GLU E 210 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL E 183 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN E 158 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA E 143 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL E 160 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.977A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 227 through 229 removed outlier: 6.495A pdb=" N VAL G 181 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N GLU G 210 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL G 183 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASN G 158 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA G 143 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL G 160 " --> pdb=" O ALA G 143 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 263 through 268 removed outlier: 6.978A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 227 through 229 removed outlier: 6.299A pdb=" N VAL B 181 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLU B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL B 183 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN B 158 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA B 143 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL B 160 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 262 through 268 removed outlier: 3.520A pdb=" N ARG B 263 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 322 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.299A pdb=" N VAL D 181 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLU D 210 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL D 183 " --> pdb=" O GLU D 210 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN D 158 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA D 143 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL D 160 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 262 through 268 removed outlier: 3.521A pdb=" N ARG D 263 " --> pdb=" O GLY D 322 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 322 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 227 through 229 removed outlier: 6.299A pdb=" N VAL F 181 " --> pdb=" O ILE F 208 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLU F 210 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL F 183 " --> pdb=" O GLU F 210 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN F 158 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA F 143 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL F 160 " --> pdb=" O ALA F 143 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 262 through 268 removed outlier: 3.521A pdb=" N ARG F 263 " --> pdb=" O GLY F 322 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY F 322 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 227 through 229 removed outlier: 6.300A pdb=" N VAL H 181 " --> pdb=" O ILE H 208 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLU H 210 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL H 183 " --> pdb=" O GLU H 210 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN H 158 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA H 143 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL H 160 " --> pdb=" O ALA H 143 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 262 through 268 removed outlier: 3.521A pdb=" N ARG H 263 " --> pdb=" O GLY H 322 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY H 322 " --> pdb=" O ARG H 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1800 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: 7.58 Time building geometry restraints manager: 7.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5601 1.34 - 1.45: 1781 1.45 - 1.57: 9706 1.57 - 1.69: 4 1.69 - 1.80: 116 Bond restraints: 17208 Sorted by residual: bond pdb=" O12 PGW E 401 " pdb=" P PGW E 401 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" O12 PGW C 401 " pdb=" P PGW C 401 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 7.98e+00 bond pdb=" O12 PGW A 401 " pdb=" P PGW A 401 " ideal model delta sigma weight residual 1.636 1.692 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" O12 PGW G 401 " pdb=" P PGW G 401 " ideal model delta sigma weight residual 1.636 1.692 -0.056 2.00e-02 2.50e+03 7.88e+00 bond pdb=" C03 PGW G 401 " pdb=" O11 PGW G 401 " ideal model delta sigma weight residual 1.412 1.362 0.050 2.00e-02 2.50e+03 6.14e+00 ... (remaining 17203 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.96: 380 106.96 - 113.74: 9917 113.74 - 120.52: 6792 120.52 - 127.31: 6025 127.31 - 134.09: 124 Bond angle restraints: 23238 Sorted by residual: angle pdb=" C SER A 273 " pdb=" N LYS A 274 " pdb=" CA LYS A 274 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.94e+00 angle pdb=" C SER E 273 " pdb=" N LYS E 274 " pdb=" CA LYS E 274 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.94e+00 angle pdb=" C SER C 273 " pdb=" N LYS C 274 " pdb=" CA LYS C 274 " ideal model delta sigma weight residual 121.54 126.19 -4.65 1.91e+00 2.74e-01 5.91e+00 angle pdb=" C SER G 273 " pdb=" N LYS G 274 " pdb=" CA LYS G 274 " ideal model delta sigma weight residual 121.54 126.17 -4.63 1.91e+00 2.74e-01 5.87e+00 angle pdb=" O13 PGW E 401 " pdb=" P PGW E 401 " pdb=" O14 PGW E 401 " ideal model delta sigma weight residual 119.81 126.95 -7.14 3.00e+00 1.11e-01 5.66e+00 ... (remaining 23233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.41: 10356 28.41 - 56.82: 112 56.82 - 85.22: 16 85.22 - 113.63: 0 113.63 - 142.04: 12 Dihedral angle restraints: 10496 sinusoidal: 4344 harmonic: 6152 Sorted by residual: dihedral pdb=" C03 PGW C 401 " pdb=" C01 PGW C 401 " pdb=" C02 PGW C 401 " pdb=" O03 PGW C 401 " ideal model delta sinusoidal sigma weight residual 295.35 153.31 142.04 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C03 PGW A 401 " pdb=" C01 PGW A 401 " pdb=" C02 PGW A 401 " pdb=" O03 PGW A 401 " ideal model delta sinusoidal sigma weight residual 295.35 153.32 142.03 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C03 PGW E 401 " pdb=" C01 PGW E 401 " pdb=" C02 PGW E 401 " pdb=" O03 PGW E 401 " ideal model delta sinusoidal sigma weight residual 295.35 153.36 141.99 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 10493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1626 0.038 - 0.077: 700 0.077 - 0.115: 303 0.115 - 0.153: 59 0.153 - 0.191: 4 Chirality restraints: 2692 Sorted by residual: chirality pdb=" CA PHE G 88 " pdb=" N PHE G 88 " pdb=" C PHE G 88 " pdb=" CB PHE G 88 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" CA PHE C 88 " pdb=" N PHE C 88 " pdb=" C PHE C 88 " pdb=" CB PHE C 88 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA PHE E 88 " pdb=" N PHE E 88 " pdb=" C PHE E 88 " pdb=" CB PHE E 88 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 2689 not shown) Planarity restraints: 3004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 47 " -0.034 2.00e-02 2.50e+03 6.72e-02 4.52e+01 pdb=" C THR C 47 " 0.116 2.00e-02 2.50e+03 pdb=" O THR C 47 " -0.043 2.00e-02 2.50e+03 pdb=" N VAL C 48 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 47 " 0.034 2.00e-02 2.50e+03 6.72e-02 4.51e+01 pdb=" C THR A 47 " -0.116 2.00e-02 2.50e+03 pdb=" O THR A 47 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL A 48 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 47 " -0.034 2.00e-02 2.50e+03 6.72e-02 4.51e+01 pdb=" C THR E 47 " 0.116 2.00e-02 2.50e+03 pdb=" O THR E 47 " -0.043 2.00e-02 2.50e+03 pdb=" N VAL E 48 " -0.039 2.00e-02 2.50e+03 ... (remaining 3001 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 5042 2.83 - 3.41: 17733 3.41 - 3.99: 30217 3.99 - 4.56: 42736 4.56 - 5.14: 65028 Nonbonded interactions: 160756 Sorted by model distance: nonbonded pdb=" OE1 GLU C 133 " pdb=" OG SER D 240 " model vdw 2.255 2.440 nonbonded pdb=" OE1 GLU A 133 " pdb=" OG SER B 240 " model vdw 2.295 2.440 nonbonded pdb=" OE1 GLU E 133 " pdb=" OG SER F 240 " model vdw 2.301 2.440 nonbonded pdb=" OG SER B 279 " pdb=" OD1 ASP B 282 " model vdw 2.331 2.440 nonbonded pdb=" NH2 ARG E 308 " pdb=" OD2 ASP F 287 " model vdw 2.331 2.520 ... (remaining 160751 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' and (resid 20 through 336 or resid 401)) selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.040 Extract box with map and model: 4.490 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 50.520 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.006 0.057 17208 Z= 0.414 Angle : 0.609 7.139 23238 Z= 0.325 Chirality : 0.050 0.191 2692 Planarity : 0.007 0.067 3004 Dihedral : 10.725 142.041 6544 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.43 % Allowed : 2.39 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 2140 helix: 0.12 (0.16), residues: 1028 sheet: 3.16 (0.26), residues: 344 loop : -1.49 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 52 HIS 0.004 0.001 HIS F 117 PHE 0.010 0.002 PHE C 88 TYR 0.015 0.002 TYR G 247 ARG 0.006 0.001 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 317 time to evaluate : 2.258 Fit side-chains REVERT: A 53 THR cc_start: 0.8572 (m) cc_final: 0.8261 (p) REVERT: C 53 THR cc_start: 0.8543 (m) cc_final: 0.8329 (p) REVERT: G 53 THR cc_start: 0.8542 (m) cc_final: 0.8335 (p) outliers start: 8 outliers final: 2 residues processed: 321 average time/residue: 1.7343 time to fit residues: 602.8610 Evaluate side-chains 148 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 248 GLU Chi-restraints excluded: chain H residue 248 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17208 Z= 0.364 Angle : 0.607 8.229 23238 Z= 0.317 Chirality : 0.049 0.179 2692 Planarity : 0.004 0.035 3004 Dihedral : 12.539 148.054 2538 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.61 % Allowed : 10.92 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.18), residues: 2140 helix: 0.45 (0.16), residues: 1036 sheet: 2.93 (0.24), residues: 336 loop : -1.80 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 52 HIS 0.004 0.001 HIS F 117 PHE 0.014 0.002 PHE E 88 TYR 0.017 0.002 TYR G 33 ARG 0.009 0.001 ARG F 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 170 time to evaluate : 1.979 Fit side-chains REVERT: A 53 THR cc_start: 0.8715 (m) cc_final: 0.8451 (p) REVERT: C 53 THR cc_start: 0.8729 (m) cc_final: 0.8468 (p) REVERT: E 250 MET cc_start: 0.8232 (mtp) cc_final: 0.7779 (mtp) REVERT: G 33 TYR cc_start: 0.7940 (t80) cc_final: 0.7719 (t80) REVERT: G 53 THR cc_start: 0.8712 (m) cc_final: 0.8449 (p) outliers start: 48 outliers final: 10 residues processed: 200 average time/residue: 1.4511 time to fit residues: 321.1455 Evaluate side-chains 152 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain G residue 150 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 chunk 208 optimal weight: 5.9990 chunk 171 optimal weight: 0.0670 chunk 191 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17208 Z= 0.139 Angle : 0.452 6.881 23238 Z= 0.234 Chirality : 0.045 0.163 2692 Planarity : 0.003 0.021 3004 Dihedral : 11.757 149.257 2532 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.85 % Allowed : 12.99 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2140 helix: 0.80 (0.16), residues: 1072 sheet: 2.80 (0.25), residues: 344 loop : -1.69 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 52 HIS 0.002 0.001 HIS D 117 PHE 0.015 0.001 PHE A 75 TYR 0.013 0.001 TYR G 33 ARG 0.005 0.000 ARG F 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 2.184 Fit side-chains REVERT: C 53 THR cc_start: 0.8653 (m) cc_final: 0.8391 (p) REVERT: G 53 THR cc_start: 0.8614 (m) cc_final: 0.8375 (p) outliers start: 34 outliers final: 10 residues processed: 183 average time/residue: 1.4914 time to fit residues: 300.5368 Evaluate side-chains 152 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 147 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 0.8980 chunk 145 optimal weight: 0.0050 chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17208 Z= 0.132 Angle : 0.437 6.900 23238 Z= 0.228 Chirality : 0.045 0.170 2692 Planarity : 0.003 0.023 3004 Dihedral : 11.307 145.482 2532 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.39 % Allowed : 13.48 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 2140 helix: 1.17 (0.17), residues: 1052 sheet: 2.85 (0.25), residues: 344 loop : -1.57 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 123 HIS 0.001 0.000 HIS F 117 PHE 0.008 0.001 PHE A 75 TYR 0.009 0.001 TYR E 51 ARG 0.005 0.000 ARG F 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 160 time to evaluate : 2.078 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 11 residues processed: 191 average time/residue: 1.6642 time to fit residues: 347.1781 Evaluate side-chains 148 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain F residue 266 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 174 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17208 Z= 0.235 Angle : 0.495 8.929 23238 Z= 0.258 Chirality : 0.046 0.182 2692 Planarity : 0.003 0.031 3004 Dihedral : 11.162 143.743 2532 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.96 % Allowed : 13.91 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 2140 helix: 1.17 (0.17), residues: 1060 sheet: 3.00 (0.25), residues: 336 loop : -1.47 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 123 HIS 0.004 0.001 HIS F 117 PHE 0.019 0.001 PHE A 75 TYR 0.010 0.001 TYR F 333 ARG 0.004 0.000 ARG E 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8259 (ptpp) REVERT: B 147 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7515 (m-40) REVERT: H 147 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7489 (m-40) outliers start: 36 outliers final: 14 residues processed: 164 average time/residue: 1.6879 time to fit residues: 302.5404 Evaluate side-chains 143 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain H residue 147 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 17208 Z= 0.322 Angle : 0.523 8.991 23238 Z= 0.272 Chirality : 0.047 0.150 2692 Planarity : 0.004 0.036 3004 Dihedral : 11.305 145.455 2532 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.45 % Rotamer: Outliers : 1.79 % Allowed : 14.51 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.19), residues: 2140 helix: 1.06 (0.16), residues: 1060 sheet: 2.86 (0.25), residues: 336 loop : -1.54 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 123 HIS 0.004 0.001 HIS F 117 PHE 0.013 0.001 PHE A 75 TYR 0.009 0.001 TYR B 333 ARG 0.004 0.000 ARG G 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 2.111 Fit side-chains REVERT: A 274 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8346 (ptpt) REVERT: B 116 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7410 (tpm-80) REVERT: D 116 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7415 (tpm-80) REVERT: H 116 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7423 (tpm-80) outliers start: 33 outliers final: 14 residues processed: 159 average time/residue: 1.7866 time to fit residues: 308.7795 Evaluate side-chains 148 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain H residue 116 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 149 optimal weight: 0.0000 chunk 172 optimal weight: 8.9990 chunk 114 optimal weight: 0.2980 chunk 204 optimal weight: 8.9990 chunk 127 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17208 Z= 0.124 Angle : 0.451 7.994 23238 Z= 0.231 Chirality : 0.044 0.144 2692 Planarity : 0.003 0.028 3004 Dihedral : 11.088 144.542 2532 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.52 % Allowed : 14.78 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 2140 helix: 1.21 (0.17), residues: 1068 sheet: 2.76 (0.26), residues: 344 loop : -1.38 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 46 HIS 0.004 0.001 HIS A 39 PHE 0.012 0.001 PHE A 75 TYR 0.007 0.001 TYR A 51 ARG 0.003 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8342 (ptpp) outliers start: 28 outliers final: 15 residues processed: 158 average time/residue: 1.7565 time to fit residues: 302.1144 Evaluate side-chains 146 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.0040 chunk 39 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 139 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17208 Z= 0.231 Angle : 0.486 8.014 23238 Z= 0.249 Chirality : 0.046 0.144 2692 Planarity : 0.003 0.033 3004 Dihedral : 11.067 143.567 2532 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.03 % Allowed : 15.71 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 2140 helix: 1.28 (0.17), residues: 1056 sheet: 2.76 (0.26), residues: 344 loop : -1.42 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 46 HIS 0.005 0.001 HIS E 39 PHE 0.030 0.001 PHE C 54 TYR 0.008 0.001 TYR E 51 ARG 0.003 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8361 (ptpt) outliers start: 19 outliers final: 12 residues processed: 143 average time/residue: 1.7643 time to fit residues: 275.3766 Evaluate side-chains 142 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 1.9990 chunk 178 optimal weight: 0.2980 chunk 190 optimal weight: 0.4980 chunk 114 optimal weight: 0.0070 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 172 optimal weight: 0.4980 chunk 180 optimal weight: 0.4980 chunk 189 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17208 Z= 0.112 Angle : 0.455 7.611 23238 Z= 0.229 Chirality : 0.044 0.147 2692 Planarity : 0.003 0.034 3004 Dihedral : 10.754 139.982 2532 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.92 % Allowed : 15.92 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 2140 helix: 1.44 (0.17), residues: 1056 sheet: 2.87 (0.26), residues: 344 loop : -1.32 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 46 HIS 0.004 0.001 HIS C 39 PHE 0.024 0.001 PHE C 54 TYR 0.007 0.001 TYR C 65 ARG 0.003 0.000 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 2.084 Fit side-chains revert: symmetry clash REVERT: C 25 LEU cc_start: 0.7798 (pp) cc_final: 0.7416 (mm) outliers start: 17 outliers final: 7 residues processed: 154 average time/residue: 1.7438 time to fit residues: 292.9477 Evaluate side-chains 133 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 161 HIS H 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17208 Z= 0.178 Angle : 0.486 8.842 23238 Z= 0.245 Chirality : 0.045 0.144 2692 Planarity : 0.003 0.036 3004 Dihedral : 10.726 138.509 2532 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.60 % Allowed : 16.25 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 2140 helix: 1.43 (0.17), residues: 1044 sheet: 2.87 (0.26), residues: 344 loop : -1.19 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 46 HIS 0.003 0.001 HIS C 39 PHE 0.033 0.001 PHE E 54 TYR 0.008 0.001 TYR E 51 ARG 0.003 0.000 ARG E 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 2.090 Fit side-chains REVERT: C 25 LEU cc_start: 0.7840 (pp) cc_final: 0.7418 (mm) outliers start: 11 outliers final: 8 residues processed: 138 average time/residue: 1.7050 time to fit residues: 257.0121 Evaluate side-chains 133 residues out of total 1840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 21 optimal weight: 0.0070 chunk 31 optimal weight: 20.0000 chunk 147 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.102069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.067650 restraints weight = 30373.269| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.80 r_work: 0.2750 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17208 Z= 0.276 Angle : 0.521 8.627 23238 Z= 0.266 Chirality : 0.047 0.144 2692 Planarity : 0.003 0.037 3004 Dihedral : 10.930 139.506 2532 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.49 % Allowed : 16.30 % Favored : 83.21 % 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: 1.04 (0.19), residues: 2140 helix: 1.32 (0.17), residues: 1044 sheet: 2.76 (0.26), residues: 344 loop : -1.27 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 46 HIS 0.004 0.001 HIS D 117 PHE 0.033 0.001 PHE E 54 TYR 0.008 0.001 TYR E 51 ARG 0.003 0.000 ARG C 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6129.90 seconds wall clock time: 109 minutes 28.59 seconds (6568.59 seconds total)