Starting phenix.real_space_refine on Thu Sep 26 23:51:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/09_2024/8gmp_40229_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/09_2024/8gmp_40229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/09_2024/8gmp_40229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/09_2024/8gmp_40229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/09_2024/8gmp_40229_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmp_40229/09_2024/8gmp_40229_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 136 5.16 5 C 9000 2.51 5 N 2216 2.21 5 O 2296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13656 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1655 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, G, F, H Time building chain proxies: 4.92, per 1000 atoms: 0.36 Number of scatterers: 13656 At special positions: 0 Unit cell: (113.848, 113.848, 98.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 P 8 15.00 O 2296 8.00 N 2216 7.00 C 9000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 161 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 0 sheets defined 70.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'C' and resid 25 through 38 removed outlier: 3.599A pdb=" N ALA C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 36 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 37 " --> pdb=" O GLN C 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 38 " --> pdb=" O MET C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Proline residue: C 60 - end of helix removed outlier: 3.543A pdb=" N LEU C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET C 103 " --> pdb=" O MET C 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 115 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 130 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE C 183 " --> pdb=" O TYR C 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN C 185 " --> pdb=" O ARG C 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 198 " --> pdb=" O LEU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 204 Processing helix chain 'C' and resid 210 through 236 removed outlier: 3.615A pdb=" N HIS C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 251 removed outlier: 3.845A pdb=" N LYS C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.543A pdb=" N LEU A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 3.815A pdb=" N MET A 103 " --> pdb=" O MET A 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE A 183 " --> pdb=" O TYR A 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 210 through 236 removed outlier: 3.615A pdb=" N HIS A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 removed outlier: 3.846A pdb=" N LYS A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 38 " --> pdb=" O MET B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Proline residue: B 60 - end of helix removed outlier: 3.543A pdb=" N LEU B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET B 103 " --> pdb=" O MET B 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B 105 " --> pdb=" O CYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 210 through 236 removed outlier: 3.615A pdb=" N HIS B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 251 removed outlier: 3.845A pdb=" N LYS B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA D 37 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 38 " --> pdb=" O MET D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Proline residue: D 60 - end of helix removed outlier: 3.543A pdb=" N LEU D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET D 103 " --> pdb=" O MET D 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 105 " --> pdb=" O CYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 130 Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 179 through 200 removed outlier: 3.679A pdb=" N ILE D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'D' and resid 210 through 236 removed outlier: 3.615A pdb=" N HIS D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 251 removed outlier: 3.845A pdb=" N LYS D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN D 249 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 37 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 38 " --> pdb=" O MET E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) Proline residue: E 60 - end of helix removed outlier: 3.543A pdb=" N LEU E 66 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET E 103 " --> pdb=" O MET E 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN E 105 " --> pdb=" O CYS E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 130 Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE E 183 " --> pdb=" O TYR E 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN E 185 " --> pdb=" O ARG E 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 192 " --> pdb=" O GLY E 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 204 Processing helix chain 'E' and resid 210 through 236 removed outlier: 3.615A pdb=" N HIS E 222 " --> pdb=" O LYS E 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP E 225 " --> pdb=" O SER E 221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 251 removed outlier: 3.845A pdb=" N LYS E 244 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN E 249 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR F 35 " --> pdb=" O SER F 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER F 36 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA F 37 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE F 38 " --> pdb=" O MET F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA F 51 " --> pdb=" O GLY F 47 " (cutoff:3.500A) Proline residue: F 60 - end of helix removed outlier: 3.543A pdb=" N LEU F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET F 103 " --> pdb=" O MET F 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN F 105 " --> pdb=" O CYS F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL F 115 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 130 Processing helix chain 'F' and resid 152 through 157 Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE F 183 " --> pdb=" O TYR F 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN F 185 " --> pdb=" O ARG F 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 192 " --> pdb=" O GLY F 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 198 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 204 Processing helix chain 'F' and resid 210 through 236 removed outlier: 3.615A pdb=" N HIS F 222 " --> pdb=" O LYS F 218 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP F 225 " --> pdb=" O SER F 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 251 removed outlier: 3.846A pdb=" N LYS F 244 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN F 249 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER G 36 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA G 37 " --> pdb=" O GLN G 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE G 38 " --> pdb=" O MET G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) Proline residue: G 60 - end of helix removed outlier: 3.543A pdb=" N LEU G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET G 103 " --> pdb=" O MET G 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN G 105 " --> pdb=" O CYS G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL G 112 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL G 115 " --> pdb=" O PRO G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 130 Processing helix chain 'G' and resid 152 through 157 Processing helix chain 'G' and resid 172 through 177 Processing helix chain 'G' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE G 183 " --> pdb=" O TYR G 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN G 185 " --> pdb=" O ARG G 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 192 " --> pdb=" O GLY G 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU G 198 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 204 Processing helix chain 'G' and resid 210 through 236 removed outlier: 3.616A pdb=" N HIS G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP G 225 " --> pdb=" O SER G 221 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU G 233 " --> pdb=" O LYS G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 251 removed outlier: 3.844A pdb=" N LYS G 244 " --> pdb=" O LYS G 240 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN G 249 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 removed outlier: 3.599A pdb=" N ALA H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA H 37 " --> pdb=" O GLN H 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE H 38 " --> pdb=" O MET H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 70 removed outlier: 4.241A pdb=" N ALA H 51 " --> pdb=" O GLY H 47 " (cutoff:3.500A) Proline residue: H 60 - end of helix removed outlier: 3.543A pdb=" N LEU H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY H 68 " --> pdb=" O LEU H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.816A pdb=" N MET H 103 " --> pdb=" O MET H 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN H 105 " --> pdb=" O CYS H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 120 removed outlier: 3.552A pdb=" N VAL H 112 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL H 115 " --> pdb=" O PRO H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 130 Processing helix chain 'H' and resid 152 through 157 Processing helix chain 'H' and resid 172 through 177 Processing helix chain 'H' and resid 179 through 200 removed outlier: 3.680A pdb=" N ILE H 183 " --> pdb=" O TYR H 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN H 185 " --> pdb=" O ARG H 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL H 192 " --> pdb=" O GLY H 188 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU H 198 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'H' and resid 210 through 236 removed outlier: 3.616A pdb=" N HIS H 222 " --> pdb=" O LYS H 218 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP H 225 " --> pdb=" O SER H 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU H 233 " --> pdb=" O LYS H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 251 removed outlier: 3.846A pdb=" N LYS H 244 " --> pdb=" O LYS H 240 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL H 245 " --> pdb=" O ALA H 241 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN H 248 " --> pdb=" O LYS H 244 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN H 249 " --> pdb=" O VAL H 245 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1947 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: 3.16 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2056 1.31 - 1.44: 3792 1.44 - 1.57: 7936 1.57 - 1.70: 16 1.70 - 1.83: 184 Bond restraints: 13984 Sorted by residual: bond pdb=" C TRP H 109 " pdb=" O TRP H 109 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.31e-02 5.83e+03 1.95e+01 bond pdb=" C TRP G 109 " pdb=" O TRP G 109 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.31e-02 5.83e+03 1.95e+01 bond pdb=" C TRP C 109 " pdb=" O TRP C 109 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.31e-02 5.83e+03 1.92e+01 bond pdb=" C TRP B 109 " pdb=" O TRP B 109 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.31e-02 5.83e+03 1.92e+01 bond pdb=" C TRP E 109 " pdb=" O TRP E 109 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.31e-02 5.83e+03 1.92e+01 ... (remaining 13979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 18776 4.00 - 7.99: 152 7.99 - 11.99: 16 11.99 - 15.99: 16 15.99 - 19.98: 8 Bond angle restraints: 18968 Sorted by residual: angle pdb=" C ASN H 41 " pdb=" N CYS H 42 " pdb=" CA CYS H 42 " ideal model delta sigma weight residual 124.01 104.03 19.98 1.84e+00 2.95e-01 1.18e+02 angle pdb=" C ASN F 41 " pdb=" N CYS F 42 " pdb=" CA CYS F 42 " ideal model delta sigma weight residual 124.01 104.06 19.95 1.84e+00 2.95e-01 1.18e+02 angle pdb=" C ASN G 41 " pdb=" N CYS G 42 " pdb=" CA CYS G 42 " ideal model delta sigma weight residual 124.01 104.07 19.94 1.84e+00 2.95e-01 1.17e+02 angle pdb=" C ASN B 41 " pdb=" N CYS B 42 " pdb=" CA CYS B 42 " ideal model delta sigma weight residual 124.01 104.07 19.94 1.84e+00 2.95e-01 1.17e+02 angle pdb=" C ASN C 41 " pdb=" N CYS C 42 " pdb=" CA CYS C 42 " ideal model delta sigma weight residual 124.01 104.07 19.94 1.84e+00 2.95e-01 1.17e+02 ... (remaining 18963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.50: 7657 20.50 - 41.00: 459 41.00 - 61.50: 234 61.50 - 82.00: 32 82.00 - 102.50: 8 Dihedral angle restraints: 8390 sinusoidal: 3294 harmonic: 5096 Sorted by residual: dihedral pdb=" CA ALA H 176 " pdb=" C ALA H 176 " pdb=" N VAL H 177 " pdb=" CA VAL H 177 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ALA G 176 " pdb=" C ALA G 176 " pdb=" N VAL G 177 " pdb=" CA VAL G 177 " ideal model delta harmonic sigma weight residual 180.00 159.23 20.77 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ALA C 176 " pdb=" C ALA C 176 " pdb=" N VAL C 177 " pdb=" CA VAL C 177 " ideal model delta harmonic sigma weight residual 180.00 159.23 20.77 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 8387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1941 0.066 - 0.133: 171 0.133 - 0.199: 24 0.199 - 0.266: 0 0.266 - 0.332: 8 Chirality restraints: 2144 Sorted by residual: chirality pdb=" CA TRP H 109 " pdb=" N TRP H 109 " pdb=" C TRP H 109 " pdb=" CB TRP H 109 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA TRP E 109 " pdb=" N TRP E 109 " pdb=" C TRP E 109 " pdb=" CB TRP E 109 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA TRP B 109 " pdb=" N TRP B 109 " pdb=" C TRP B 109 " pdb=" CB TRP B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 2141 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 60 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO F 61 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO F 61 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 61 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 60 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO H 61 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 60 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.75e+00 pdb=" N PRO B 61 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " 0.034 5.00e-02 4.00e+02 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 86 2.61 - 3.18: 11171 3.18 - 3.75: 18581 3.75 - 4.33: 27041 4.33 - 4.90: 44504 Nonbonded interactions: 101383 Sorted by model distance: nonbonded pdb=" SG CYS D 42 " pdb=" SG CYS D 127 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS H 44 " pdb=" SG CYS H 161 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS D 44 " pdb=" SG CYS D 161 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS G 44 " pdb=" SG CYS G 161 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS B 44 " pdb=" SG CYS B 161 " model vdw 2.035 3.760 ... (remaining 101378 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' 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 26.340 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.030 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 0.086 13984 Z= 0.402 Angle : 1.086 19.983 18968 Z= 0.577 Chirality : 0.046 0.332 2144 Planarity : 0.007 0.060 2328 Dihedral : 17.177 102.504 5056 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.96 % Allowed : 4.14 % Favored : 92.90 % 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: -6.76 (0.13), residues: 1680 helix: -4.65 (0.06), residues: 1232 sheet: None (None), residues: 0 loop : -3.04 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP H 109 HIS 0.002 0.001 HIS H 238 PHE 0.010 0.001 PHE A 125 TYR 0.009 0.001 TYR D 179 ARG 0.003 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 276 time to evaluate : 1.452 Fit side-chains REVERT: C 74 ASN cc_start: 0.7605 (m110) cc_final: 0.7168 (t0) REVERT: C 77 MET cc_start: 0.6827 (mtt) cc_final: 0.6621 (mtt) REVERT: C 100 PHE cc_start: 0.6993 (t80) cc_final: 0.6664 (t80) REVERT: A 74 ASN cc_start: 0.7516 (m110) cc_final: 0.6999 (t0) REVERT: A 100 PHE cc_start: 0.6955 (t80) cc_final: 0.6698 (t80) REVERT: B 74 ASN cc_start: 0.7610 (m110) cc_final: 0.7168 (t0) REVERT: B 77 MET cc_start: 0.6829 (mtt) cc_final: 0.6626 (mtt) REVERT: B 100 PHE cc_start: 0.6994 (t80) cc_final: 0.6666 (t80) REVERT: D 74 ASN cc_start: 0.7519 (m110) cc_final: 0.6997 (t0) REVERT: D 100 PHE cc_start: 0.6960 (t80) cc_final: 0.6701 (t80) REVERT: E 74 ASN cc_start: 0.7607 (m110) cc_final: 0.7162 (t0) REVERT: E 77 MET cc_start: 0.6829 (mtt) cc_final: 0.6625 (mtt) REVERT: E 100 PHE cc_start: 0.6994 (t80) cc_final: 0.6665 (t80) REVERT: F 74 ASN cc_start: 0.7518 (m110) cc_final: 0.6996 (t0) REVERT: F 100 PHE cc_start: 0.6958 (t80) cc_final: 0.6700 (t80) REVERT: G 74 ASN cc_start: 0.7606 (m110) cc_final: 0.7162 (t0) REVERT: G 77 MET cc_start: 0.6829 (mtt) cc_final: 0.6623 (mtt) REVERT: G 100 PHE cc_start: 0.6994 (t80) cc_final: 0.6666 (t80) REVERT: H 74 ASN cc_start: 0.7515 (m110) cc_final: 0.6997 (t0) REVERT: H 100 PHE cc_start: 0.6953 (t80) cc_final: 0.6695 (t80) outliers start: 40 outliers final: 8 residues processed: 304 average time/residue: 1.0683 time to fit residues: 358.8260 Evaluate side-chains 236 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 228 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 131 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.8980 chunk 127 optimal weight: 0.0050 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 0.0270 chunk 68 optimal weight: 8.9990 chunk 131 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 overall best weight: 0.4852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN A 105 GLN B 105 GLN D 105 GLN E 105 GLN F 105 GLN G 105 GLN H 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13984 Z= 0.175 Angle : 0.664 7.196 18968 Z= 0.343 Chirality : 0.041 0.130 2144 Planarity : 0.006 0.045 2328 Dihedral : 15.342 75.698 2208 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.44 % Allowed : 13.31 % Favored : 84.25 % 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: -4.26 (0.16), residues: 1680 helix: -2.60 (0.11), residues: 1208 sheet: None (None), residues: 0 loop : -2.88 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 114 HIS 0.002 0.001 HIS A 222 PHE 0.013 0.001 PHE B 209 TYR 0.013 0.001 TYR G 98 ARG 0.003 0.000 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 245 time to evaluate : 1.591 Fit side-chains revert: symmetry clash REVERT: C 154 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7364 (ttm-80) REVERT: C 229 LYS cc_start: 0.8113 (mttp) cc_final: 0.7880 (ttmm) REVERT: A 100 PHE cc_start: 0.6834 (t80) cc_final: 0.6584 (t80) REVERT: A 103 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.7045 (ttt) REVERT: A 229 LYS cc_start: 0.8228 (mttp) cc_final: 0.7705 (ttpp) REVERT: B 154 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7342 (ttm-80) REVERT: B 229 LYS cc_start: 0.8115 (mttp) cc_final: 0.7881 (ttmm) REVERT: D 100 PHE cc_start: 0.6841 (t80) cc_final: 0.6603 (t80) REVERT: D 103 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.7047 (ttt) REVERT: D 229 LYS cc_start: 0.8230 (mttp) cc_final: 0.7711 (ttpp) REVERT: E 154 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7341 (ttm-80) REVERT: E 229 LYS cc_start: 0.8109 (mttp) cc_final: 0.7875 (ttmm) REVERT: F 100 PHE cc_start: 0.6838 (t80) cc_final: 0.6586 (t80) REVERT: F 103 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.7043 (ttt) REVERT: F 229 LYS cc_start: 0.8223 (mttp) cc_final: 0.7708 (ttpp) REVERT: G 154 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7344 (ttm-80) REVERT: G 229 LYS cc_start: 0.8110 (mttp) cc_final: 0.7878 (ttmm) REVERT: H 100 PHE cc_start: 0.6829 (t80) cc_final: 0.6592 (t80) REVERT: H 103 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.7041 (ttt) REVERT: H 229 LYS cc_start: 0.8227 (mttp) cc_final: 0.7707 (ttpp) outliers start: 33 outliers final: 13 residues processed: 250 average time/residue: 1.0995 time to fit residues: 302.5792 Evaluate side-chains 244 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 227 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 254 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 0.0070 chunk 126 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 chunk 42 optimal weight: 30.0000 chunk 152 optimal weight: 0.0000 chunk 165 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 0.0030 chunk 122 optimal weight: 1.9990 overall best weight: 0.5614 ------------------------------------------------------------------------------- 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: 0.7733 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13984 Z= 0.169 Angle : 0.562 6.202 18968 Z= 0.292 Chirality : 0.039 0.122 2144 Planarity : 0.006 0.044 2328 Dihedral : 14.182 77.330 2204 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.22 % Allowed : 15.68 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.19), residues: 1680 helix: -1.27 (0.14), residues: 1256 sheet: None (None), residues: 0 loop : -3.17 (0.24), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 114 HIS 0.001 0.000 HIS A 238 PHE 0.012 0.001 PHE G 100 TYR 0.011 0.001 TYR E 98 ARG 0.002 0.000 ARG E 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 233 time to evaluate : 1.528 Fit side-chains revert: symmetry clash REVERT: C 154 ARG cc_start: 0.7840 (ttm110) cc_final: 0.7327 (ttm-80) REVERT: A 100 PHE cc_start: 0.6897 (t80) cc_final: 0.6689 (t80) REVERT: A 103 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7272 (ttt) REVERT: A 163 GLU cc_start: 0.6951 (pm20) cc_final: 0.6658 (pm20) REVERT: B 154 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7290 (ttm-80) REVERT: D 100 PHE cc_start: 0.6905 (t80) cc_final: 0.6692 (t80) REVERT: D 103 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7266 (ttt) REVERT: D 163 GLU cc_start: 0.6961 (pm20) cc_final: 0.6682 (pm20) REVERT: E 154 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7287 (ttm-80) REVERT: F 100 PHE cc_start: 0.6900 (t80) cc_final: 0.6687 (t80) REVERT: F 103 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7267 (ttt) REVERT: G 154 ARG cc_start: 0.7804 (ttm110) cc_final: 0.7288 (ttm-80) REVERT: H 100 PHE cc_start: 0.6907 (t80) cc_final: 0.6694 (t80) REVERT: H 103 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7255 (ttt) REVERT: H 163 GLU cc_start: 0.6945 (pm20) cc_final: 0.6657 (pm20) outliers start: 30 outliers final: 9 residues processed: 236 average time/residue: 1.1586 time to fit residues: 299.8204 Evaluate side-chains 239 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 226 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain H residue 103 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13984 Z= 0.183 Angle : 0.564 6.074 18968 Z= 0.290 Chirality : 0.039 0.130 2144 Planarity : 0.006 0.048 2328 Dihedral : 13.789 75.609 2200 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.99 % Allowed : 17.31 % Favored : 78.70 % 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: -2.01 (0.20), residues: 1680 helix: -0.65 (0.15), residues: 1256 sheet: None (None), residues: 0 loop : -3.15 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 114 HIS 0.001 0.000 HIS C 238 PHE 0.007 0.001 PHE C 125 TYR 0.009 0.001 TYR B 98 ARG 0.002 0.000 ARG G 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 244 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: A 100 PHE cc_start: 0.6858 (t80) cc_final: 0.6652 (t80) REVERT: A 103 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7218 (ttt) REVERT: B 154 ARG cc_start: 0.7855 (ttm110) cc_final: 0.7275 (ttm-80) REVERT: B 163 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.5743 (mp0) REVERT: B 233 GLU cc_start: 0.7910 (mp0) cc_final: 0.7567 (mp0) REVERT: D 100 PHE cc_start: 0.6842 (t80) cc_final: 0.6635 (t80) REVERT: D 103 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7211 (ttt) REVERT: E 163 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5737 (mp0) REVERT: F 100 PHE cc_start: 0.6865 (t80) cc_final: 0.6653 (t80) REVERT: F 103 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7210 (ttt) REVERT: G 163 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.5739 (mp0) REVERT: H 100 PHE cc_start: 0.6863 (t80) cc_final: 0.6656 (t80) REVERT: H 103 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7225 (ttt) outliers start: 54 outliers final: 30 residues processed: 251 average time/residue: 1.1896 time to fit residues: 326.5338 Evaluate side-chains 273 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 251 PHE Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 251 PHE Chi-restraints excluded: chain H residue 254 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN A 74 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN D 74 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN F 74 ASN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN H 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13984 Z= 0.220 Angle : 0.575 6.137 18968 Z= 0.296 Chirality : 0.040 0.141 2144 Planarity : 0.006 0.053 2328 Dihedral : 13.886 77.010 2200 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.99 % Allowed : 19.08 % Favored : 76.92 % 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: -1.81 (0.20), residues: 1680 helix: -0.48 (0.15), residues: 1280 sheet: None (None), residues: 0 loop : -3.33 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 114 HIS 0.001 0.000 HIS A 238 PHE 0.009 0.001 PHE C 125 TYR 0.008 0.001 TYR E 98 ARG 0.002 0.000 ARG C 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 252 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7399 (m-40) cc_final: 0.6922 (t0) REVERT: A 74 ASN cc_start: 0.7257 (m-40) cc_final: 0.6617 (t0) REVERT: A 103 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7304 (ttt) REVERT: B 74 ASN cc_start: 0.7397 (m-40) cc_final: 0.6912 (t0) REVERT: B 163 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6065 (mp0) REVERT: B 233 GLU cc_start: 0.7760 (mp0) cc_final: 0.7481 (mp0) REVERT: D 74 ASN cc_start: 0.7258 (m-40) cc_final: 0.6614 (t0) REVERT: D 103 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7298 (ttt) REVERT: E 74 ASN cc_start: 0.7389 (m-40) cc_final: 0.6909 (t0) REVERT: E 163 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6049 (mp0) REVERT: F 74 ASN cc_start: 0.7247 (m-40) cc_final: 0.6610 (t0) REVERT: F 103 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7323 (ttt) REVERT: G 74 ASN cc_start: 0.7398 (m-40) cc_final: 0.6917 (t0) REVERT: G 163 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6048 (mp0) REVERT: H 74 ASN cc_start: 0.7239 (m-40) cc_final: 0.6609 (t0) REVERT: H 103 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7268 (ttt) outliers start: 54 outliers final: 37 residues processed: 265 average time/residue: 1.1668 time to fit residues: 338.9800 Evaluate side-chains 288 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 244 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 251 PHE Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 251 PHE Chi-restraints excluded: chain H residue 254 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.0870 chunk 146 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 13 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13984 Z= 0.154 Angle : 0.519 6.081 18968 Z= 0.267 Chirality : 0.038 0.124 2144 Planarity : 0.006 0.051 2328 Dihedral : 13.701 77.498 2200 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.96 % Allowed : 20.93 % Favored : 76.11 % 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: -1.11 (0.21), residues: 1680 helix: 0.11 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -3.32 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 114 HIS 0.000 0.000 HIS H 238 PHE 0.015 0.001 PHE D 100 TYR 0.008 0.001 TYR C 98 ARG 0.001 0.000 ARG G 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 259 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7325 (m-40) cc_final: 0.6627 (t0) REVERT: A 74 ASN cc_start: 0.7203 (m-40) cc_final: 0.6569 (t0) REVERT: A 103 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7144 (ttt) REVERT: B 74 ASN cc_start: 0.7319 (m-40) cc_final: 0.6618 (t0) REVERT: B 154 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7202 (ttm-80) REVERT: B 163 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6075 (mp0) REVERT: D 74 ASN cc_start: 0.7204 (m-40) cc_final: 0.6561 (t0) REVERT: D 103 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7141 (ttt) REVERT: E 74 ASN cc_start: 0.7314 (m-40) cc_final: 0.6616 (t0) REVERT: E 154 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7200 (ttm-80) REVERT: E 163 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6045 (mp0) REVERT: F 74 ASN cc_start: 0.7171 (m-40) cc_final: 0.6561 (t0) REVERT: F 103 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7133 (ttt) REVERT: G 74 ASN cc_start: 0.7335 (m-40) cc_final: 0.6650 (t0) REVERT: G 154 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7204 (ttm-80) REVERT: G 163 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6048 (mp0) REVERT: H 74 ASN cc_start: 0.7169 (m-40) cc_final: 0.6561 (t0) REVERT: H 103 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7133 (ttt) outliers start: 40 outliers final: 25 residues processed: 260 average time/residue: 1.2024 time to fit residues: 341.2586 Evaluate side-chains 276 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 244 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 251 PHE Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 218 LYS Chi-restraints excluded: chain H residue 226 ILE Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN E 49 ASN G 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13984 Z= 0.228 Angle : 0.571 6.153 18968 Z= 0.292 Chirality : 0.041 0.138 2144 Planarity : 0.006 0.055 2328 Dihedral : 13.658 79.144 2200 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.14 % Allowed : 20.49 % Favored : 75.37 % 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: -0.98 (0.20), residues: 1680 helix: 0.16 (0.15), residues: 1280 sheet: None (None), residues: 0 loop : -3.17 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 189 HIS 0.000 0.000 HIS B 238 PHE 0.009 0.001 PHE C 125 TYR 0.016 0.001 TYR A 98 ARG 0.003 0.000 ARG E 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 251 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7369 (m-40) cc_final: 0.6632 (t0) REVERT: A 71 MET cc_start: 0.7184 (mtp) cc_final: 0.6648 (ttm) REVERT: A 74 ASN cc_start: 0.7249 (m-40) cc_final: 0.6585 (t0) REVERT: B 74 ASN cc_start: 0.7359 (m-40) cc_final: 0.6625 (t0) REVERT: B 163 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6230 (mp0) REVERT: D 71 MET cc_start: 0.7193 (mtp) cc_final: 0.6653 (ttm) REVERT: D 74 ASN cc_start: 0.7252 (m-40) cc_final: 0.6585 (t0) REVERT: E 74 ASN cc_start: 0.7353 (m-40) cc_final: 0.6624 (t0) REVERT: E 163 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6356 (mp0) REVERT: F 71 MET cc_start: 0.7186 (mtp) cc_final: 0.6648 (ttm) REVERT: F 74 ASN cc_start: 0.7246 (m-40) cc_final: 0.6572 (t0) REVERT: G 74 ASN cc_start: 0.7375 (m-40) cc_final: 0.6651 (t0) REVERT: G 163 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6328 (mp0) REVERT: H 71 MET cc_start: 0.7184 (mtp) cc_final: 0.6651 (ttm) REVERT: H 74 ASN cc_start: 0.7231 (m-40) cc_final: 0.6568 (t0) outliers start: 56 outliers final: 32 residues processed: 266 average time/residue: 1.1755 time to fit residues: 342.7429 Evaluate side-chains 271 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 236 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 218 LYS Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.0010 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 102 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 147 optimal weight: 30.0000 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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: 0.7697 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13984 Z= 0.149 Angle : 0.515 6.002 18968 Z= 0.266 Chirality : 0.037 0.111 2144 Planarity : 0.006 0.052 2328 Dihedral : 13.257 80.089 2200 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.74 % Allowed : 21.67 % Favored : 75.59 % 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: -0.20 (0.21), residues: 1680 helix: 0.80 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -3.14 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 114 HIS 0.001 0.000 HIS A 222 PHE 0.013 0.001 PHE D 100 TYR 0.010 0.001 TYR F 98 ARG 0.001 0.000 ARG E 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 237 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7346 (m-40) cc_final: 0.6623 (t0) REVERT: C 154 ARG cc_start: 0.7780 (ttm110) cc_final: 0.7191 (ttm-80) REVERT: A 74 ASN cc_start: 0.7170 (m-40) cc_final: 0.6604 (t0) REVERT: B 74 ASN cc_start: 0.7338 (m-40) cc_final: 0.6612 (t0) REVERT: B 154 ARG cc_start: 0.7688 (ttm110) cc_final: 0.7143 (ttm-80) REVERT: B 163 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: D 74 ASN cc_start: 0.7174 (m-40) cc_final: 0.6589 (t0) REVERT: E 74 ASN cc_start: 0.7335 (m-40) cc_final: 0.6611 (t0) REVERT: E 154 ARG cc_start: 0.7642 (ttm110) cc_final: 0.7051 (ttm-80) REVERT: E 163 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6385 (mp0) REVERT: F 74 ASN cc_start: 0.7177 (m-40) cc_final: 0.6603 (t0) REVERT: G 74 ASN cc_start: 0.7356 (m-40) cc_final: 0.6624 (t0) REVERT: G 154 ARG cc_start: 0.7654 (ttm110) cc_final: 0.7075 (ttm-80) REVERT: G 163 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: H 74 ASN cc_start: 0.7158 (m-40) cc_final: 0.6572 (t0) outliers start: 37 outliers final: 17 residues processed: 238 average time/residue: 1.2424 time to fit residues: 323.9209 Evaluate side-chains 254 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 234 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 136 optimal weight: 0.0980 chunk 142 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 159 optimal weight: 0.0040 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13984 Z= 0.144 Angle : 0.506 6.038 18968 Z= 0.260 Chirality : 0.037 0.114 2144 Planarity : 0.006 0.051 2328 Dihedral : 12.943 82.300 2200 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.41 % Allowed : 22.41 % Favored : 76.18 % 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: 0.52 (0.22), residues: 1680 helix: 1.34 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -2.96 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 114 HIS 0.000 0.000 HIS E 238 PHE 0.019 0.001 PHE H 209 TYR 0.010 0.001 TYR C 48 ARG 0.001 0.000 ARG E 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 236 time to evaluate : 1.550 Fit side-chains REVERT: C 74 ASN cc_start: 0.7222 (m-40) cc_final: 0.6567 (t0) REVERT: C 154 ARG cc_start: 0.7587 (ttm110) cc_final: 0.7034 (ttm-80) REVERT: A 74 ASN cc_start: 0.7166 (m-40) cc_final: 0.6461 (t0) REVERT: B 74 ASN cc_start: 0.7191 (m-40) cc_final: 0.6540 (t0) REVERT: B 154 ARG cc_start: 0.7538 (ttm110) cc_final: 0.6995 (ttm-80) REVERT: B 163 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: D 74 ASN cc_start: 0.7165 (m-40) cc_final: 0.6457 (t0) REVERT: E 74 ASN cc_start: 0.7165 (m-40) cc_final: 0.6530 (t0) REVERT: E 154 ARG cc_start: 0.7535 (ttm110) cc_final: 0.6976 (ttm-80) REVERT: F 74 ASN cc_start: 0.7173 (m-40) cc_final: 0.6462 (t0) REVERT: G 74 ASN cc_start: 0.7202 (m-40) cc_final: 0.6564 (t0) REVERT: G 154 ARG cc_start: 0.7535 (ttm110) cc_final: 0.6978 (ttm-80) REVERT: H 74 ASN cc_start: 0.7171 (m-40) cc_final: 0.6462 (t0) outliers start: 19 outliers final: 9 residues processed: 239 average time/residue: 1.2279 time to fit residues: 320.5342 Evaluate side-chains 235 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 225 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 0.0050 chunk 110 optimal weight: 8.9990 chunk 167 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 105 optimal weight: 30.0000 chunk 141 optimal weight: 0.9980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN D 49 ASN F 49 ASN H 49 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13984 Z= 0.176 Angle : 0.529 6.103 18968 Z= 0.272 Chirality : 0.039 0.122 2144 Planarity : 0.006 0.053 2328 Dihedral : 12.980 83.642 2200 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.48 % Allowed : 22.49 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1680 helix: 1.36 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -2.95 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 114 HIS 0.000 0.000 HIS H 222 PHE 0.024 0.001 PHE B 209 TYR 0.008 0.001 TYR H 98 ARG 0.001 0.000 ARG B 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 229 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: C 74 ASN cc_start: 0.7221 (m-40) cc_final: 0.6564 (t0) REVERT: C 154 ARG cc_start: 0.7676 (ttm110) cc_final: 0.7113 (ttm-80) REVERT: A 74 ASN cc_start: 0.7151 (m-40) cc_final: 0.6442 (t0) REVERT: B 74 ASN cc_start: 0.7220 (m-40) cc_final: 0.6566 (t0) REVERT: B 154 ARG cc_start: 0.7585 (ttm110) cc_final: 0.7042 (ttm-80) REVERT: B 163 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6467 (mp0) REVERT: D 74 ASN cc_start: 0.7146 (m-40) cc_final: 0.6449 (t0) REVERT: E 74 ASN cc_start: 0.7217 (m-40) cc_final: 0.6564 (t0) REVERT: E 154 ARG cc_start: 0.7598 (ttm110) cc_final: 0.7045 (ttm-80) REVERT: F 74 ASN cc_start: 0.7150 (m-40) cc_final: 0.6447 (t0) REVERT: G 74 ASN cc_start: 0.7232 (m-40) cc_final: 0.6575 (t0) REVERT: G 154 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7048 (ttm-80) REVERT: H 74 ASN cc_start: 0.7140 (m-40) cc_final: 0.6440 (t0) outliers start: 20 outliers final: 14 residues processed: 237 average time/residue: 1.2162 time to fit residues: 316.8092 Evaluate side-chains 243 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 228 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 251 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.200540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.148780 restraints weight = 13707.900| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.72 r_work: 0.3507 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13984 Z= 0.185 Angle : 0.533 6.113 18968 Z= 0.275 Chirality : 0.039 0.130 2144 Planarity : 0.006 0.053 2328 Dihedral : 13.008 84.921 2200 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.11 % Allowed : 22.78 % Favored : 76.11 % 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: 0.61 (0.22), residues: 1680 helix: 1.40 (0.15), residues: 1272 sheet: None (None), residues: 0 loop : -2.90 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 114 HIS 0.000 0.000 HIS F 222 PHE 0.017 0.001 PHE A 209 TYR 0.013 0.001 TYR C 48 ARG 0.001 0.000 ARG B 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5391.76 seconds wall clock time: 95 minutes 3.15 seconds (5703.15 seconds total)