Starting phenix.real_space_refine on Sat Mar 16 01:42:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5u_4420/03_2024/6i5u_4420.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5u_4420/03_2024/6i5u_4420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5u_4420/03_2024/6i5u_4420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5u_4420/03_2024/6i5u_4420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5u_4420/03_2024/6i5u_4420.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5u_4420/03_2024/6i5u_4420.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 8550 2.51 5 N 2286 2.21 5 O 2442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 225": "NH1" <-> "NH2" Residue "F ARG 297": "NH1" <-> "NH2" Residue "E ARG 225": "NH1" <-> "NH2" Residue "E ARG 297": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13356 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "C" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "B" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "A" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 510 residue: pdb=" N ARG F 37 " occ=0.97 ... (9 atoms not shown) pdb=" NH2 ARG F 37 " occ=0.93 residue: pdb=" N ALA F 38 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA F 38 " occ=0.97 residue: pdb=" N VAL F 41 " occ=0.97 ... (5 atoms not shown) pdb=" CG2 VAL F 41 " occ=0.93 residue: pdb=" N GLN F 42 " occ=0.97 ... (7 atoms not shown) pdb=" NE2 GLN F 42 " occ=0.95 residue: pdb=" N ALA F 43 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA F 43 " occ=0.97 residue: pdb=" N VAL F 46 " occ=0.97 ... (5 atoms not shown) pdb=" CG2 VAL F 46 " occ=0.94 residue: pdb=" N ALA F 52 " occ=0.96 ... (3 atoms not shown) pdb=" CB ALA F 52 " occ=0.93 residue: pdb=" N LYS F 56 " occ=0.97 ... (7 atoms not shown) pdb=" NZ LYS F 56 " occ=0.94 residue: pdb=" N ALA F 57 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA F 57 " occ=0.97 residue: pdb=" N LEU F 60 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU F 60 " occ=0.80 residue: pdb=" N GLU F 63 " occ=0.97 ... (7 atoms not shown) pdb=" OE2 GLU F 63 " occ=0.80 residue: pdb=" N ALA F 64 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA F 64 " occ=0.97 ... (remaining 498 not shown) Time building chain proxies: 6.98, per 1000 atoms: 0.52 Number of scatterers: 13356 At special positions: 0 Unit cell: (117.3, 132.6, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 2442 8.00 N 2286 7.00 C 8550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 2.3 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 21 sheets defined 22.8% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'F' and resid 54 through 66 Processing helix chain 'F' and resid 96 through 108 removed outlier: 4.371A pdb=" N ARG F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASP F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 127 removed outlier: 3.511A pdb=" N GLU F 119 " --> pdb=" O GLY F 115 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG F 120 " --> pdb=" O PRO F 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 210 removed outlier: 3.854A pdb=" N ARG F 206 " --> pdb=" O MET F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 213 No H-bonds generated for 'chain 'F' and resid 211 through 213' Processing helix chain 'F' and resid 225 through 239 removed outlier: 4.437A pdb=" N LEU F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA F 230 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 66 Processing helix chain 'E' and resid 96 through 108 removed outlier: 4.371A pdb=" N ARG E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASP E 102 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 127 removed outlier: 3.511A pdb=" N GLU E 119 " --> pdb=" O GLY E 115 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG E 120 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 210 removed outlier: 3.855A pdb=" N ARG E 206 " --> pdb=" O MET E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 225 through 239 removed outlier: 4.437A pdb=" N LEU E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 230 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 66 Processing helix chain 'D' and resid 96 through 108 removed outlier: 4.371A pdb=" N ARG D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASP D 102 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.511A pdb=" N GLU D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG D 120 " --> pdb=" O PRO D 116 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU D 121 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 210 removed outlier: 3.854A pdb=" N ARG D 206 " --> pdb=" O MET D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 225 through 239 removed outlier: 4.438A pdb=" N LEU D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 Processing helix chain 'C' and resid 96 through 108 removed outlier: 4.372A pdb=" N ARG C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASP C 102 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.511A pdb=" N GLU C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG C 120 " --> pdb=" O PRO C 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 210 removed outlier: 3.854A pdb=" N ARG C 206 " --> pdb=" O MET C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 225 through 239 removed outlier: 4.438A pdb=" N LEU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 96 through 108 removed outlier: 4.372A pdb=" N ARG B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASP B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 127 removed outlier: 3.511A pdb=" N GLU B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 210 removed outlier: 3.854A pdb=" N ARG B 206 " --> pdb=" O MET B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 225 through 239 removed outlier: 4.437A pdb=" N LEU B 229 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 96 through 108 removed outlier: 4.371A pdb=" N ARG A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASP A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.510A pdb=" N GLU A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 120 " --> pdb=" O PRO A 116 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 210 removed outlier: 3.854A pdb=" N ARG A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 225 through 239 removed outlier: 4.437A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 157 through 160 removed outlier: 4.320A pdb=" N GLY F 159 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE F 150 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU F 71 " --> pdb=" O ARG F 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'F' and resid 186 through 187 removed outlier: 6.568A pdb=" N TYR F 217 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA F 246 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA F 219 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE F 283 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 330 through 334 removed outlier: 3.531A pdb=" N SER E 331 " --> pdb=" O ASN F 333 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER F 331 " --> pdb=" O ASN E 333 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N SER D 343 " --> pdb=" O PHE F 330 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU F 332 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LYS D 345 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE F 334 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 157 through 160 removed outlier: 4.320A pdb=" N GLY E 159 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE E 150 " --> pdb=" O GLY E 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 71 " --> pdb=" O ARG E 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'E' and resid 186 through 187 removed outlier: 6.568A pdb=" N TYR E 217 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA E 246 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA E 219 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE E 283 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 342 through 345 removed outlier: 3.531A pdb=" N SER C 331 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 331 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N SER B 343 " --> pdb=" O PHE D 330 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU D 332 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LYS B 345 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE D 334 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 157 through 160 removed outlier: 4.320A pdb=" N GLY D 159 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D 150 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D 71 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AB2, first strand: chain 'D' and resid 186 through 187 removed outlier: 6.567A pdb=" N TYR D 217 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA D 246 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA D 219 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE D 283 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 157 through 160 removed outlier: 4.319A pdb=" N GLY C 159 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 150 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 71 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AB5, first strand: chain 'C' and resid 186 through 187 removed outlier: 6.568A pdb=" N TYR C 217 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA C 246 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA C 219 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE C 283 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 342 through 345 removed outlier: 3.547A pdb=" N SER A 331 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 331 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 157 through 160 removed outlier: 4.319A pdb=" N GLY B 159 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 150 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 71 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AB9, first strand: chain 'B' and resid 186 through 187 removed outlier: 6.568A pdb=" N TYR B 217 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA B 246 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA B 219 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE B 283 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 157 through 160 removed outlier: 4.319A pdb=" N GLY A 159 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 150 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 71 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AC3, first strand: chain 'A' and resid 186 through 187 removed outlier: 6.569A pdb=" N TYR A 217 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA A 246 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA A 219 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE A 283 " --> pdb=" O LEU A 291 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 972 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: 3.26 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4311 1.34 - 1.46: 2757 1.46 - 1.58: 6474 1.58 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 13656 Sorted by residual: bond pdb=" CA HIS C 323 " pdb=" C HIS C 323 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.34e-02 5.57e+03 4.37e+00 bond pdb=" CA HIS D 323 " pdb=" C HIS D 323 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.34e-02 5.57e+03 4.29e+00 bond pdb=" CA HIS E 323 " pdb=" C HIS E 323 " ideal model delta sigma weight residual 1.523 1.551 -0.027 1.34e-02 5.57e+03 4.20e+00 bond pdb=" CA HIS A 323 " pdb=" C HIS A 323 " ideal model delta sigma weight residual 1.523 1.551 -0.027 1.34e-02 5.57e+03 4.18e+00 bond pdb=" CA HIS B 323 " pdb=" C HIS B 323 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.34e-02 5.57e+03 4.15e+00 ... (remaining 13651 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.67: 456 106.67 - 113.50: 7227 113.50 - 120.33: 5236 120.33 - 127.16: 5405 127.16 - 134.00: 162 Bond angle restraints: 18486 Sorted by residual: angle pdb=" C VAL A 320 " pdb=" N VAL A 321 " pdb=" CA VAL A 321 " ideal model delta sigma weight residual 121.97 130.87 -8.90 1.80e+00 3.09e-01 2.45e+01 angle pdb=" C VAL C 320 " pdb=" N VAL C 321 " pdb=" CA VAL C 321 " ideal model delta sigma weight residual 121.97 130.87 -8.90 1.80e+00 3.09e-01 2.44e+01 angle pdb=" C VAL F 320 " pdb=" N VAL F 321 " pdb=" CA VAL F 321 " ideal model delta sigma weight residual 121.97 130.86 -8.89 1.80e+00 3.09e-01 2.44e+01 angle pdb=" C VAL B 320 " pdb=" N VAL B 321 " pdb=" CA VAL B 321 " ideal model delta sigma weight residual 121.97 130.85 -8.88 1.80e+00 3.09e-01 2.43e+01 angle pdb=" C VAL E 320 " pdb=" N VAL E 321 " pdb=" CA VAL E 321 " ideal model delta sigma weight residual 121.97 130.79 -8.82 1.80e+00 3.09e-01 2.40e+01 ... (remaining 18481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.50: 7576 14.50 - 28.99: 428 28.99 - 43.48: 90 43.48 - 57.98: 6 57.98 - 72.47: 6 Dihedral angle restraints: 8106 sinusoidal: 3162 harmonic: 4944 Sorted by residual: dihedral pdb=" CA GLY A 322 " pdb=" C GLY A 322 " pdb=" N HIS A 323 " pdb=" CA HIS A 323 " ideal model delta harmonic sigma weight residual -180.00 -107.53 -72.47 0 5.00e+00 4.00e-02 2.10e+02 dihedral pdb=" CA GLY C 322 " pdb=" C GLY C 322 " pdb=" N HIS C 323 " pdb=" CA HIS C 323 " ideal model delta harmonic sigma weight residual -180.00 -107.53 -72.47 0 5.00e+00 4.00e-02 2.10e+02 dihedral pdb=" CA GLY B 322 " pdb=" C GLY B 322 " pdb=" N HIS B 323 " pdb=" CA HIS B 323 " ideal model delta harmonic sigma weight residual -180.00 -107.53 -72.47 0 5.00e+00 4.00e-02 2.10e+02 ... (remaining 8103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1530 0.061 - 0.122: 457 0.122 - 0.182: 29 0.182 - 0.243: 24 0.243 - 0.304: 18 Chirality restraints: 2058 Sorted by residual: chirality pdb=" CB VAL B 320 " pdb=" CA VAL B 320 " pdb=" CG1 VAL B 320 " pdb=" CG2 VAL B 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB VAL F 320 " pdb=" CA VAL F 320 " pdb=" CG1 VAL F 320 " pdb=" CG2 VAL F 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB VAL C 320 " pdb=" CA VAL C 320 " pdb=" CG1 VAL C 320 " pdb=" CG2 VAL C 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 2055 not shown) Planarity restraints: 2370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 47 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C PHE E 47 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE E 47 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR E 48 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 47 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C PHE A 47 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE A 47 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR A 48 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 47 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C PHE C 47 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE C 47 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR C 48 " 0.013 2.00e-02 2.50e+03 ... (remaining 2367 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4512 2.86 - 3.37: 11075 3.37 - 3.88: 20030 3.88 - 4.39: 22434 4.39 - 4.90: 39873 Nonbonded interactions: 97924 Sorted by model distance: nonbonded pdb=" OE1 GLU F 89 " pdb=" OG1 THR F 96 " model vdw 2.350 2.440 nonbonded pdb=" OE1 GLU E 89 " pdb=" OG1 THR E 96 " model vdw 2.350 2.440 nonbonded pdb=" OE1 GLU D 89 " pdb=" OG1 THR D 96 " model vdw 2.350 2.440 nonbonded pdb=" OE1 GLU C 89 " pdb=" OG1 THR C 96 " model vdw 2.350 2.440 nonbonded pdb=" OE1 GLU B 89 " pdb=" OG1 THR B 96 " model vdw 2.350 2.440 ... (remaining 97919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 4.410 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 33.210 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.005 0.053 13656 Z= 0.367 Angle : 1.059 12.457 18486 Z= 0.570 Chirality : 0.063 0.304 2058 Planarity : 0.008 0.054 2370 Dihedral : 9.934 72.475 4950 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.68 % Favored : 85.61 % Rotamer: Outliers : 0.43 % Allowed : 5.15 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.10 % 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: -5.63 (0.14), residues: 1710 helix: -3.77 (0.15), residues: 402 sheet: -3.64 (0.23), residues: 324 loop : -3.89 (0.14), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 198 HIS 0.007 0.003 HIS C 234 PHE 0.011 0.002 PHE D 316 TYR 0.029 0.003 TYR E 324 ARG 0.004 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 473 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 310 ASP cc_start: 0.8184 (t0) cc_final: 0.7903 (t0) REVERT: F 317 ASP cc_start: 0.8328 (m-30) cc_final: 0.8103 (m-30) REVERT: F 339 ARG cc_start: 0.7139 (mtt-85) cc_final: 0.6655 (ttp-170) REVERT: E 285 SER cc_start: 0.9097 (t) cc_final: 0.8613 (p) REVERT: E 295 ASN cc_start: 0.7828 (t0) cc_final: 0.7595 (t0) REVERT: E 310 ASP cc_start: 0.7858 (t0) cc_final: 0.6989 (t0) REVERT: E 335 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8133 (mtt-85) REVERT: D 215 GLU cc_start: 0.7877 (pm20) cc_final: 0.7528 (pm20) REVERT: D 310 ASP cc_start: 0.8262 (t0) cc_final: 0.7756 (t0) REVERT: C 54 LEU cc_start: 0.8674 (tp) cc_final: 0.8460 (tp) REVERT: C 285 SER cc_start: 0.9198 (t) cc_final: 0.8742 (p) REVERT: C 295 ASN cc_start: 0.7868 (t0) cc_final: 0.7642 (t0) REVERT: C 310 ASP cc_start: 0.8116 (t0) cc_final: 0.7165 (t0) REVERT: C 335 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.8319 (mtt-85) REVERT: B 138 GLU cc_start: 0.8411 (pt0) cc_final: 0.8159 (pt0) REVERT: B 310 ASP cc_start: 0.8236 (t0) cc_final: 0.7802 (t0) REVERT: B 315 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8859 (mtmt) REVERT: A 295 ASN cc_start: 0.7863 (t0) cc_final: 0.7597 (t0) REVERT: A 310 ASP cc_start: 0.8126 (t0) cc_final: 0.7343 (t0) REVERT: A 335 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.8089 (mtt-85) REVERT: A 343 SER cc_start: 0.9027 (m) cc_final: 0.8691 (p) outliers start: 6 outliers final: 1 residues processed: 479 average time/residue: 0.3397 time to fit residues: 214.8797 Evaluate side-chains 242 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN F 248 GLN E 200 ASN E 323 HIS D 42 GLN D 200 ASN D 248 GLN C 161 HIS C 200 ASN B 42 GLN B 200 ASN B 337 HIS A 200 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 13656 Z= 0.375 Angle : 0.792 10.222 18486 Z= 0.406 Chirality : 0.050 0.216 2058 Planarity : 0.006 0.042 2370 Dihedral : 6.455 47.616 1903 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 1.05 % Allowed : 15.32 % Favored : 83.63 % Rotamer: Outliers : 4.51 % Allowed : 13.09 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -4.74 (0.16), residues: 1710 helix: -2.59 (0.20), residues: 438 sheet: -2.33 (0.28), residues: 342 loop : -3.90 (0.15), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 198 HIS 0.009 0.003 HIS B 323 PHE 0.015 0.002 PHE F 316 TYR 0.022 0.002 TYR C 296 ARG 0.005 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 242 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 138 GLU cc_start: 0.8462 (pt0) cc_final: 0.8226 (pt0) REVERT: F 317 ASP cc_start: 0.8242 (m-30) cc_final: 0.7933 (m-30) REVERT: F 336 GLU cc_start: 0.6947 (tt0) cc_final: 0.6606 (mt-10) REVERT: F 339 ARG cc_start: 0.7398 (mtt-85) cc_final: 0.6740 (ttp-170) REVERT: E 295 ASN cc_start: 0.8240 (t0) cc_final: 0.7933 (t0) REVERT: E 297 ARG cc_start: 0.7866 (mpp-170) cc_final: 0.7396 (ptt90) REVERT: E 310 ASP cc_start: 0.7930 (t0) cc_final: 0.7032 (t0) REVERT: E 335 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8163 (mtt-85) REVERT: D 215 GLU cc_start: 0.8017 (pm20) cc_final: 0.7607 (pm20) REVERT: D 283 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.8996 (mt) REVERT: C 117 GLU cc_start: 0.7589 (mp0) cc_final: 0.7371 (mt-10) REVERT: C 295 ASN cc_start: 0.8327 (t0) cc_final: 0.7842 (t0) REVERT: C 310 ASP cc_start: 0.8107 (t0) cc_final: 0.6889 (t0) REVERT: B 283 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8948 (mt) REVERT: A 295 ASN cc_start: 0.8273 (t0) cc_final: 0.7732 (t0) REVERT: A 310 ASP cc_start: 0.8117 (t0) cc_final: 0.7221 (t0) REVERT: A 339 ARG cc_start: 0.4257 (ttt180) cc_final: 0.3680 (ttt-90) REVERT: A 343 SER cc_start: 0.9026 (m) cc_final: 0.8498 (p) outliers start: 63 outliers final: 38 residues processed: 292 average time/residue: 0.2692 time to fit residues: 110.3495 Evaluate side-chains 212 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 197 CYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 227 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN B 248 GLN A 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13656 Z= 0.270 Angle : 0.718 10.879 18486 Z= 0.359 Chirality : 0.046 0.186 2058 Planarity : 0.005 0.042 2370 Dihedral : 6.157 48.818 1903 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.99 % Allowed : 14.62 % Favored : 84.39 % Rotamer: Outliers : 4.94 % Allowed : 13.88 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -4.29 (0.17), residues: 1710 helix: -1.74 (0.23), residues: 408 sheet: -2.16 (0.27), residues: 342 loop : -3.80 (0.15), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 198 HIS 0.012 0.002 HIS B 323 PHE 0.012 0.001 PHE D 316 TYR 0.017 0.001 TYR C 296 ARG 0.004 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 200 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: F 317 ASP cc_start: 0.8038 (m-30) cc_final: 0.7687 (m-30) REVERT: F 324 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7856 (t80) REVERT: F 339 ARG cc_start: 0.7313 (mtt-85) cc_final: 0.6562 (ttp-170) REVERT: F 342 VAL cc_start: 0.9591 (t) cc_final: 0.9348 (p) REVERT: E 94 SER cc_start: 0.7907 (m) cc_final: 0.7545 (p) REVERT: E 140 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7168 (mt-10) REVERT: E 283 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8886 (mt) REVERT: E 295 ASN cc_start: 0.8241 (t0) cc_final: 0.7889 (t0) REVERT: E 297 ARG cc_start: 0.7854 (mpp-170) cc_final: 0.7240 (ppt170) REVERT: E 310 ASP cc_start: 0.7940 (t0) cc_final: 0.7052 (t0) REVERT: D 138 GLU cc_start: 0.8429 (pt0) cc_final: 0.7709 (pt0) REVERT: D 215 GLU cc_start: 0.7816 (pm20) cc_final: 0.7385 (pm20) REVERT: D 336 GLU cc_start: 0.6533 (tt0) cc_final: 0.6253 (mt-10) REVERT: C 283 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8911 (mt) REVERT: C 295 ASN cc_start: 0.8371 (t0) cc_final: 0.7902 (t0) REVERT: C 310 ASP cc_start: 0.8107 (t0) cc_final: 0.7103 (t0) REVERT: C 317 ASP cc_start: 0.7526 (m-30) cc_final: 0.7301 (m-30) REVERT: B 283 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.9007 (mt) REVERT: A 138 GLU cc_start: 0.8259 (pt0) cc_final: 0.7981 (pt0) REVERT: A 140 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7177 (mt-10) REVERT: A 283 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8925 (mt) REVERT: A 287 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8777 (mt) REVERT: A 295 ASN cc_start: 0.8272 (t0) cc_final: 0.7741 (t0) REVERT: A 329 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8711 (t) REVERT: A 339 ARG cc_start: 0.4451 (ttt180) cc_final: 0.3262 (ttt180) REVERT: A 343 SER cc_start: 0.8859 (m) cc_final: 0.8435 (p) outliers start: 69 outliers final: 42 residues processed: 255 average time/residue: 0.2544 time to fit residues: 92.6579 Evaluate side-chains 215 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 166 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 197 CYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 329 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 162 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS D 42 GLN C 107 HIS C 323 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13656 Z= 0.277 Angle : 0.702 10.043 18486 Z= 0.354 Chirality : 0.046 0.188 2058 Planarity : 0.005 0.040 2370 Dihedral : 6.052 53.737 1903 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 1.05 % Allowed : 15.09 % Favored : 83.86 % Rotamer: Outliers : 6.01 % Allowed : 14.02 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -4.00 (0.18), residues: 1710 helix: -1.46 (0.24), residues: 414 sheet: -1.96 (0.28), residues: 354 loop : -3.65 (0.15), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 198 HIS 0.012 0.002 HIS B 323 PHE 0.011 0.001 PHE D 316 TYR 0.016 0.001 TYR C 296 ARG 0.009 0.000 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 171 time to evaluate : 1.469 Fit side-chains REVERT: F 317 ASP cc_start: 0.7995 (m-30) cc_final: 0.7608 (m-30) REVERT: F 324 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7843 (t80) REVERT: F 339 ARG cc_start: 0.7278 (mtt-85) cc_final: 0.6420 (ttp-170) REVERT: F 342 VAL cc_start: 0.9592 (t) cc_final: 0.9367 (p) REVERT: E 94 SER cc_start: 0.7966 (m) cc_final: 0.7674 (p) REVERT: E 123 LEU cc_start: 0.8422 (mm) cc_final: 0.7813 (pp) REVERT: E 283 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8822 (mt) REVERT: E 295 ASN cc_start: 0.8306 (t0) cc_final: 0.7630 (t0) REVERT: D 283 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8902 (mt) REVERT: D 336 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6361 (mt-10) REVERT: C 283 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8882 (mt) REVERT: C 287 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8782 (mt) REVERT: C 295 ASN cc_start: 0.8426 (t0) cc_final: 0.7934 (t0) REVERT: B 283 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8958 (mt) REVERT: A 87 THR cc_start: 0.9184 (p) cc_final: 0.8934 (t) REVERT: A 140 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7149 (mt-10) REVERT: A 287 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8671 (mt) REVERT: A 295 ASN cc_start: 0.8388 (t0) cc_final: 0.8154 (t0) REVERT: A 297 ARG cc_start: 0.7641 (mpp-170) cc_final: 0.6961 (ppt170) REVERT: A 310 ASP cc_start: 0.8145 (t0) cc_final: 0.7236 (t0) REVERT: A 339 ARG cc_start: 0.3873 (ttt180) cc_final: 0.3415 (ttt180) REVERT: A 343 SER cc_start: 0.8840 (m) cc_final: 0.8450 (p) outliers start: 84 outliers final: 53 residues processed: 240 average time/residue: 0.2375 time to fit residues: 83.7947 Evaluate side-chains 209 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 148 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 197 CYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 40 optimal weight: 0.3980 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 107 HIS B 107 HIS B 248 GLN A 107 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13656 Z= 0.343 Angle : 0.736 10.480 18486 Z= 0.375 Chirality : 0.047 0.215 2058 Planarity : 0.005 0.039 2370 Dihedral : 6.252 57.749 1903 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.82 % Allowed : 16.32 % Favored : 82.87 % Rotamer: Outliers : 6.22 % Allowed : 14.88 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.18), residues: 1710 helix: -1.71 (0.23), residues: 444 sheet: -1.72 (0.27), residues: 384 loop : -3.66 (0.16), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 198 HIS 0.010 0.002 HIS B 323 PHE 0.012 0.002 PHE B 330 TYR 0.016 0.001 TYR C 296 ARG 0.006 0.000 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 170 time to evaluate : 1.483 Fit side-chains REVERT: F 317 ASP cc_start: 0.7930 (m-30) cc_final: 0.7572 (m-30) REVERT: F 324 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7951 (t80) REVERT: F 336 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6826 (mt-10) REVERT: F 342 VAL cc_start: 0.9593 (t) cc_final: 0.9364 (p) REVERT: E 283 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8830 (mt) REVERT: E 295 ASN cc_start: 0.8366 (t0) cc_final: 0.7705 (t0) REVERT: D 283 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8840 (mt) REVERT: D 324 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8158 (t80) REVERT: D 336 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6471 (mt-10) REVERT: C 287 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8737 (mt) REVERT: C 295 ASN cc_start: 0.8528 (t0) cc_final: 0.8003 (t0) REVERT: C 310 ASP cc_start: 0.8163 (t0) cc_final: 0.7167 (t0) REVERT: C 324 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.7707 (t80) REVERT: B 283 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8880 (mt) REVERT: B 324 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8290 (t80) REVERT: A 87 THR cc_start: 0.9201 (p) cc_final: 0.8958 (t) REVERT: A 94 SER cc_start: 0.7795 (m) cc_final: 0.7234 (p) REVERT: A 287 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8762 (mt) REVERT: A 295 ASN cc_start: 0.8430 (t0) cc_final: 0.8142 (t0) REVERT: A 297 ARG cc_start: 0.7838 (mpp-170) cc_final: 0.7093 (ppt170) REVERT: A 339 ARG cc_start: 0.3619 (ttt180) cc_final: 0.2940 (ttt180) REVERT: A 343 SER cc_start: 0.8872 (m) cc_final: 0.8464 (p) outliers start: 87 outliers final: 56 residues processed: 235 average time/residue: 0.2435 time to fit residues: 83.8456 Evaluate side-chains 224 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 157 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 197 CYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13656 Z= 0.256 Angle : 0.690 10.692 18486 Z= 0.347 Chirality : 0.046 0.215 2058 Planarity : 0.005 0.040 2370 Dihedral : 5.862 48.501 1902 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 1.05 % Allowed : 14.97 % Favored : 83.98 % Rotamer: Outliers : 5.44 % Allowed : 15.88 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.18), residues: 1710 helix: -1.27 (0.25), residues: 414 sheet: -1.57 (0.29), residues: 354 loop : -3.59 (0.16), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 198 HIS 0.012 0.002 HIS B 323 PHE 0.011 0.001 PHE D 330 TYR 0.014 0.001 TYR C 296 ARG 0.005 0.000 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 173 time to evaluate : 1.459 Fit side-chains REVERT: F 317 ASP cc_start: 0.7934 (m-30) cc_final: 0.7568 (m-30) REVERT: F 324 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.7935 (t80) REVERT: F 342 VAL cc_start: 0.9599 (t) cc_final: 0.9376 (p) REVERT: E 283 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8812 (mt) REVERT: E 295 ASN cc_start: 0.8337 (t0) cc_final: 0.7706 (t0) REVERT: D 283 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8831 (mt) REVERT: D 324 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.8080 (t80) REVERT: D 336 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6454 (mt-10) REVERT: C 283 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8863 (mt) REVERT: C 287 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8751 (mt) REVERT: C 295 ASN cc_start: 0.8518 (t0) cc_final: 0.8012 (t0) REVERT: C 324 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.7724 (t80) REVERT: B 283 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8955 (mt) REVERT: B 324 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.8301 (t80) REVERT: A 87 THR cc_start: 0.9171 (p) cc_final: 0.8905 (t) REVERT: A 94 SER cc_start: 0.7777 (m) cc_final: 0.7312 (p) REVERT: A 140 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7148 (mt-10) REVERT: A 287 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8631 (mt) REVERT: A 295 ASN cc_start: 0.8411 (t0) cc_final: 0.8175 (t0) REVERT: A 297 ARG cc_start: 0.7857 (mpp-170) cc_final: 0.7131 (ppt170) REVERT: A 310 ASP cc_start: 0.8130 (t0) cc_final: 0.7249 (t0) REVERT: A 339 ARG cc_start: 0.3620 (ttt180) cc_final: 0.2899 (ttt180) REVERT: A 343 SER cc_start: 0.8828 (m) cc_final: 0.8461 (p) outliers start: 76 outliers final: 49 residues processed: 232 average time/residue: 0.2348 time to fit residues: 80.6206 Evaluate side-chains 216 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 156 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 197 CYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13656 Z= 0.211 Angle : 0.660 9.696 18486 Z= 0.330 Chirality : 0.045 0.181 2058 Planarity : 0.004 0.041 2370 Dihedral : 5.656 48.073 1902 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.99 % Allowed : 14.09 % Favored : 84.91 % Rotamer: Outliers : 4.08 % Allowed : 17.38 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.18), residues: 1710 helix: -1.07 (0.26), residues: 414 sheet: -1.52 (0.29), residues: 354 loop : -3.48 (0.16), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 228 HIS 0.012 0.002 HIS B 323 PHE 0.009 0.001 PHE A 330 TYR 0.015 0.001 TYR C 296 ARG 0.004 0.000 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 169 time to evaluate : 1.289 Fit side-chains REVERT: F 317 ASP cc_start: 0.7857 (m-30) cc_final: 0.7438 (m-30) REVERT: F 324 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7913 (t80) REVERT: F 336 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6796 (mt-10) REVERT: F 342 VAL cc_start: 0.9609 (t) cc_final: 0.9384 (p) REVERT: E 140 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7326 (mt-10) REVERT: E 295 ASN cc_start: 0.8326 (t0) cc_final: 0.7607 (p0) REVERT: E 297 ARG cc_start: 0.7936 (mtm-85) cc_final: 0.7611 (ppt170) REVERT: D 283 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8892 (mt) REVERT: D 324 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.8132 (t80) REVERT: D 336 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6491 (mt-10) REVERT: C 287 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8636 (mt) REVERT: C 295 ASN cc_start: 0.8494 (t0) cc_final: 0.8027 (t0) REVERT: C 310 ASP cc_start: 0.8132 (t0) cc_final: 0.7196 (t0) REVERT: C 324 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.7786 (t80) REVERT: B 169 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9085 (tm) REVERT: A 87 THR cc_start: 0.9135 (p) cc_final: 0.8860 (t) REVERT: A 94 SER cc_start: 0.7766 (m) cc_final: 0.7338 (p) REVERT: A 140 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7100 (mt-10) REVERT: A 197 CYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8735 (p) REVERT: A 295 ASN cc_start: 0.8380 (t0) cc_final: 0.7601 (p0) REVERT: A 297 ARG cc_start: 0.7865 (mpp-170) cc_final: 0.7172 (ppt170) REVERT: A 339 ARG cc_start: 0.3616 (ttt180) cc_final: 0.2999 (ttt180) REVERT: A 343 SER cc_start: 0.8819 (m) cc_final: 0.8503 (p) outliers start: 57 outliers final: 34 residues processed: 217 average time/residue: 0.2392 time to fit residues: 75.9400 Evaluate side-chains 198 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 155 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 333 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13656 Z= 0.271 Angle : 0.694 9.343 18486 Z= 0.350 Chirality : 0.046 0.207 2058 Planarity : 0.004 0.038 2370 Dihedral : 5.776 48.556 1902 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.99 % Allowed : 14.97 % Favored : 84.04 % Rotamer: Outliers : 5.51 % Allowed : 15.95 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.18), residues: 1710 helix: -1.07 (0.25), residues: 414 sheet: -1.52 (0.29), residues: 354 loop : -3.44 (0.16), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 198 HIS 0.011 0.002 HIS B 323 PHE 0.010 0.001 PHE B 316 TYR 0.014 0.001 TYR C 296 ARG 0.004 0.000 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 165 time to evaluate : 1.489 Fit side-chains REVERT: F 317 ASP cc_start: 0.7889 (m-30) cc_final: 0.7507 (m-30) REVERT: F 324 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7943 (t80) REVERT: F 336 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6840 (mt-10) REVERT: F 342 VAL cc_start: 0.9604 (t) cc_final: 0.9398 (p) REVERT: E 140 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7305 (mt-10) REVERT: E 283 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8807 (mt) REVERT: E 295 ASN cc_start: 0.8324 (t0) cc_final: 0.7350 (p0) REVERT: E 297 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7645 (ppt170) REVERT: D 169 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9130 (tm) REVERT: D 283 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8863 (mt) REVERT: D 324 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.8182 (t80) REVERT: D 336 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6485 (mt-10) REVERT: C 283 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8836 (mt) REVERT: C 287 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8695 (mt) REVERT: C 295 ASN cc_start: 0.8508 (t0) cc_final: 0.8040 (t0) REVERT: C 324 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.7832 (t80) REVERT: A 87 THR cc_start: 0.9177 (p) cc_final: 0.8936 (t) REVERT: A 94 SER cc_start: 0.7841 (m) cc_final: 0.7435 (p) REVERT: A 283 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8840 (mt) REVERT: A 287 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8688 (mt) REVERT: A 295 ASN cc_start: 0.8362 (t0) cc_final: 0.7641 (p0) REVERT: A 297 ARG cc_start: 0.7875 (mpp-170) cc_final: 0.7254 (ppt170) REVERT: A 339 ARG cc_start: 0.3690 (ttt180) cc_final: 0.2988 (ttt-90) REVERT: A 343 SER cc_start: 0.8851 (m) cc_final: 0.8486 (p) outliers start: 77 outliers final: 52 residues processed: 226 average time/residue: 0.2416 time to fit residues: 80.4970 Evaluate side-chains 224 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 160 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 333 ASN 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: 20.0000 chunk 150 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN B 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13656 Z= 0.296 Angle : 0.718 10.751 18486 Z= 0.363 Chirality : 0.046 0.202 2058 Planarity : 0.005 0.037 2370 Dihedral : 5.862 49.404 1902 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.99 % Allowed : 15.26 % Favored : 83.74 % Rotamer: Outliers : 5.01 % Allowed : 17.02 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.19), residues: 1710 helix: -1.36 (0.24), residues: 444 sheet: -1.60 (0.27), residues: 384 loop : -3.47 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 198 HIS 0.011 0.002 HIS B 323 PHE 0.010 0.001 PHE B 316 TYR 0.014 0.001 TYR C 296 ARG 0.004 0.000 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 160 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: F 317 ASP cc_start: 0.7891 (m-30) cc_final: 0.7503 (m-30) REVERT: F 324 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7965 (t80) REVERT: F 336 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6872 (mt-10) REVERT: E 140 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7147 (mt-10) REVERT: E 283 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8816 (mt) REVERT: E 295 ASN cc_start: 0.8336 (t0) cc_final: 0.7291 (p0) REVERT: E 297 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7687 (ppt170) REVERT: D 169 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9141 (tm) REVERT: D 283 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8852 (mt) REVERT: D 324 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8185 (t80) REVERT: D 336 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6528 (mt-10) REVERT: C 283 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8836 (mt) REVERT: C 287 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8618 (mt) REVERT: C 295 ASN cc_start: 0.8532 (t0) cc_final: 0.8062 (t0) REVERT: C 310 ASP cc_start: 0.8149 (t0) cc_final: 0.7215 (t0) REVERT: C 324 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.7824 (t80) REVERT: A 87 THR cc_start: 0.9186 (p) cc_final: 0.8939 (t) REVERT: A 94 SER cc_start: 0.7870 (m) cc_final: 0.7455 (p) REVERT: A 140 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7148 (mt-10) REVERT: A 283 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8841 (mt) REVERT: A 287 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8723 (mt) REVERT: A 295 ASN cc_start: 0.8381 (t0) cc_final: 0.7679 (p0) REVERT: A 297 ARG cc_start: 0.7883 (mpp-170) cc_final: 0.7280 (ppt170) REVERT: A 339 ARG cc_start: 0.3602 (ttt180) cc_final: 0.2651 (ttt-90) REVERT: A 343 SER cc_start: 0.8853 (m) cc_final: 0.8477 (p) outliers start: 70 outliers final: 54 residues processed: 218 average time/residue: 0.2410 time to fit residues: 76.8313 Evaluate side-chains 219 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 153 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 333 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 GLN D 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13656 Z= 0.360 Angle : 0.757 10.680 18486 Z= 0.386 Chirality : 0.048 0.216 2058 Planarity : 0.005 0.037 2370 Dihedral : 6.096 49.666 1902 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.99 % Allowed : 16.55 % Favored : 82.46 % Rotamer: Outliers : 4.86 % Allowed : 17.10 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.18), residues: 1710 helix: -1.45 (0.24), residues: 444 sheet: -1.70 (0.27), residues: 384 loop : -3.54 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 198 HIS 0.011 0.002 HIS B 323 PHE 0.012 0.002 PHE D 316 TYR 0.015 0.001 TYR B 324 ARG 0.004 0.000 ARG E 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 160 time to evaluate : 1.534 Fit side-chains revert: symmetry clash REVERT: F 225 ARG cc_start: 0.7342 (mpt-90) cc_final: 0.7073 (mpt-90) REVERT: F 317 ASP cc_start: 0.7956 (m-30) cc_final: 0.7590 (m-30) REVERT: F 324 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7982 (t80) REVERT: F 336 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6903 (mt-10) REVERT: E 140 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7189 (mt-10) REVERT: E 283 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8840 (mt) REVERT: E 295 ASN cc_start: 0.8370 (t0) cc_final: 0.7794 (t0) REVERT: D 169 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9192 (tm) REVERT: D 283 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8821 (mt) REVERT: D 324 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.8205 (t80) REVERT: D 336 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6603 (mt-10) REVERT: C 283 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8882 (mt) REVERT: C 287 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8713 (mt) REVERT: C 295 ASN cc_start: 0.8565 (t0) cc_final: 0.8051 (t0) REVERT: C 324 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.7748 (t80) REVERT: A 87 THR cc_start: 0.9225 (p) cc_final: 0.8987 (t) REVERT: A 94 SER cc_start: 0.7911 (m) cc_final: 0.7547 (p) REVERT: A 140 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7159 (mt-10) REVERT: A 295 ASN cc_start: 0.8409 (t0) cc_final: 0.7644 (p0) REVERT: A 297 ARG cc_start: 0.7935 (mpp-170) cc_final: 0.7374 (ppt170) REVERT: A 339 ARG cc_start: 0.3671 (ttt180) cc_final: 0.2879 (ttt-90) REVERT: A 343 SER cc_start: 0.8879 (m) cc_final: 0.8463 (p) outliers start: 68 outliers final: 55 residues processed: 213 average time/residue: 0.2373 time to fit residues: 74.1493 Evaluate side-chains 219 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 154 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 333 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 137 optimal weight: 0.0570 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 overall best weight: 1.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 248 GLN D 42 GLN D 248 GLN B 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.108080 restraints weight = 20525.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110536 restraints weight = 13713.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.112186 restraints weight = 10479.591| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13656 Z= 0.176 Angle : 0.658 10.739 18486 Z= 0.329 Chirality : 0.044 0.193 2058 Planarity : 0.004 0.039 2370 Dihedral : 5.487 46.959 1902 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.87 % Favored : 87.08 % Rotamer: Outliers : 3.29 % Allowed : 18.96 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.19), residues: 1710 helix: -0.84 (0.26), residues: 414 sheet: -1.56 (0.28), residues: 354 loop : -3.34 (0.17), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 228 HIS 0.011 0.002 HIS B 323 PHE 0.009 0.001 PHE A 330 TYR 0.013 0.001 TYR C 296 ARG 0.004 0.000 ARG E 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2538.96 seconds wall clock time: 46 minutes 37.06 seconds (2797.06 seconds total)