Starting phenix.real_space_refine on Thu Mar 5 03:49:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f94_31497/03_2026/7f94_31497.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f94_31497/03_2026/7f94_31497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f94_31497/03_2026/7f94_31497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f94_31497/03_2026/7f94_31497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f94_31497/03_2026/7f94_31497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f94_31497/03_2026/7f94_31497.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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 96 5.16 5 C 12780 2.51 5 N 3048 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19128 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Chain: "G" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, H, I, J, K, L Time building chain proxies: 2.66, per 1000 atoms: 0.14 Number of scatterers: 19128 At special positions: 0 Unit cell: (101.925, 105.975, 174.15, 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 96 16.00 O 3204 8.00 N 3048 7.00 C 12780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 818.9 milliseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 72.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 3.625A pdb=" N LYS A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.774A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 89 through 109 removed outlier: 3.669A pdb=" N LEU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.972A pdb=" N ARG A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 234 removed outlier: 3.698A pdb=" N PHE A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 15 removed outlier: 4.107A pdb=" N GLY G 8 " --> pdb=" O TRP G 4 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU G 10 " --> pdb=" O ALA G 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP G 12 " --> pdb=" O GLY G 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN G 15 " --> pdb=" O LEU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 40 removed outlier: 3.770A pdb=" N LYS G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.929A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 removed outlier: 3.822A pdb=" N SER G 69 " --> pdb=" O CYS G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 105 Proline residue: G 88 - end of helix removed outlier: 3.559A pdb=" N LYS G 105 " --> pdb=" O ARG G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 177 Processing helix chain 'G' and resid 204 through 233 removed outlier: 3.810A pdb=" N ILE G 208 " --> pdb=" O THR G 204 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 14 removed outlier: 3.623A pdb=" N LYS B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 10 " --> pdb=" O ALA B 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 31 Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.775A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 85 Processing helix chain 'B' and resid 89 through 109 removed outlier: 3.669A pdb=" N LEU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 177 removed outlier: 3.972A pdb=" N ARG B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 234 removed outlier: 3.697A pdb=" N PHE B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 15 removed outlier: 4.108A pdb=" N GLY L 8 " --> pdb=" O TRP L 4 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU L 10 " --> pdb=" O ALA L 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP L 12 " --> pdb=" O GLY L 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN L 15 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 40 removed outlier: 3.771A pdb=" N LYS L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TRP L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 removed outlier: 3.929A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.823A pdb=" N SER L 69 " --> pdb=" O CYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 105 Proline residue: L 88 - end of helix removed outlier: 3.559A pdb=" N LYS L 105 " --> pdb=" O ARG L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 177 Processing helix chain 'L' and resid 204 through 233 removed outlier: 3.810A pdb=" N ILE L 208 " --> pdb=" O THR L 204 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE L 209 " --> pdb=" O GLU L 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN L 224 " --> pdb=" O SER L 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 14 removed outlier: 3.624A pdb=" N LYS C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.774A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 85 Processing helix chain 'C' and resid 89 through 109 removed outlier: 3.670A pdb=" N LEU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 177 removed outlier: 3.973A pdb=" N ARG C 153 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 234 removed outlier: 3.697A pdb=" N PHE C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 15 removed outlier: 4.108A pdb=" N GLY K 8 " --> pdb=" O TRP K 4 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS K 9 " --> pdb=" O SER K 5 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU K 10 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP K 12 " --> pdb=" O GLY K 8 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 40 removed outlier: 3.770A pdb=" N LYS K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 removed outlier: 3.929A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 removed outlier: 3.822A pdb=" N SER K 69 " --> pdb=" O CYS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 105 Proline residue: K 88 - end of helix removed outlier: 3.559A pdb=" N LYS K 105 " --> pdb=" O ARG K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 177 Processing helix chain 'K' and resid 204 through 233 removed outlier: 3.811A pdb=" N ILE K 208 " --> pdb=" O THR K 204 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE K 209 " --> pdb=" O GLU K 205 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN K 224 " --> pdb=" O SER K 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 14 removed outlier: 3.625A pdb=" N LYS D 9 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 10 " --> pdb=" O ALA D 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 31 Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.774A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 85 Processing helix chain 'D' and resid 89 through 109 removed outlier: 3.669A pdb=" N LEU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 177 removed outlier: 3.972A pdb=" N ARG D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 234 removed outlier: 3.698A pdb=" N PHE D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 15 removed outlier: 4.108A pdb=" N GLY J 8 " --> pdb=" O TRP J 4 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU J 10 " --> pdb=" O ALA J 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP J 12 " --> pdb=" O GLY J 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN J 15 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 40 removed outlier: 3.770A pdb=" N LYS J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.929A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 removed outlier: 3.822A pdb=" N SER J 69 " --> pdb=" O CYS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 105 Proline residue: J 88 - end of helix removed outlier: 3.559A pdb=" N LYS J 105 " --> pdb=" O ARG J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 177 Processing helix chain 'J' and resid 204 through 233 removed outlier: 3.811A pdb=" N ILE J 208 " --> pdb=" O THR J 204 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE J 209 " --> pdb=" O GLU J 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN J 224 " --> pdb=" O SER J 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 14 removed outlier: 3.624A pdb=" N LYS E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.774A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 85 Processing helix chain 'E' and resid 89 through 109 removed outlier: 3.669A pdb=" N LEU E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 177 removed outlier: 3.972A pdb=" N ARG E 153 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 234 removed outlier: 3.697A pdb=" N PHE E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN E 224 " --> pdb=" O SER E 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 15 removed outlier: 4.108A pdb=" N GLY I 8 " --> pdb=" O TRP I 4 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS I 9 " --> pdb=" O SER I 5 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU I 10 " --> pdb=" O ALA I 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP I 12 " --> pdb=" O GLY I 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN I 15 " --> pdb=" O LEU I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 40 removed outlier: 3.771A pdb=" N LYS I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.929A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.822A pdb=" N SER I 69 " --> pdb=" O CYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 105 Proline residue: I 88 - end of helix removed outlier: 3.559A pdb=" N LYS I 105 " --> pdb=" O ARG I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 177 Processing helix chain 'I' and resid 204 through 233 removed outlier: 3.810A pdb=" N ILE I 208 " --> pdb=" O THR I 204 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN I 224 " --> pdb=" O SER I 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 14 removed outlier: 3.624A pdb=" N LYS F 9 " --> pdb=" O SER F 5 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU F 10 " --> pdb=" O ALA F 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 31 Processing helix chain 'F' and resid 33 through 40 Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.774A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 85 Processing helix chain 'F' and resid 89 through 109 removed outlier: 3.669A pdb=" N LEU F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 177 removed outlier: 3.972A pdb=" N ARG F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 234 removed outlier: 3.698A pdb=" N PHE F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN F 224 " --> pdb=" O SER F 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 225 " --> pdb=" O LEU F 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 15 removed outlier: 4.107A pdb=" N GLY H 8 " --> pdb=" O TRP H 4 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU H 10 " --> pdb=" O ALA H 6 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP H 12 " --> pdb=" O GLY H 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN H 15 " --> pdb=" O LEU H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 40 removed outlier: 3.770A pdb=" N LYS H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.928A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 removed outlier: 3.822A pdb=" N SER H 69 " --> pdb=" O CYS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 105 Proline residue: H 88 - end of helix removed outlier: 3.558A pdb=" N LYS H 105 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 177 Processing helix chain 'H' and resid 204 through 233 removed outlier: 3.810A pdb=" N ILE H 208 " --> pdb=" O THR H 204 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN H 224 " --> pdb=" O SER H 220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.609A pdb=" N ARG G 53 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.609A pdb=" N ARG L 53 " --> pdb=" O PHE L 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.622A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.609A pdb=" N ARG K 53 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.610A pdb=" N ARG J 53 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.623A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.609A pdb=" N ARG I 53 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.624A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.609A pdb=" N ARG H 53 " --> pdb=" O PHE H 199 " (cutoff:3.500A) 1200 hydrogen bonds defined for protein. 3564 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: 2.51 Time building geometry restraints manager: 1.84 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: 5542 1.34 - 1.46: 4046 1.46 - 1.57: 9936 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 19644 Sorted by residual: bond pdb=" CA VAL I 87 " pdb=" CB VAL I 87 " ideal model delta sigma weight residual 1.537 1.544 -0.007 5.00e-03 4.00e+04 2.23e+00 bond pdb=" CA VAL C 87 " pdb=" C VAL C 87 " ideal model delta sigma weight residual 1.524 1.540 -0.015 1.05e-02 9.07e+03 2.13e+00 bond pdb=" CA VAL K 87 " pdb=" CB VAL K 87 " ideal model delta sigma weight residual 1.537 1.544 -0.007 5.00e-03 4.00e+04 2.07e+00 bond pdb=" CA VAL J 87 " pdb=" CB VAL J 87 " ideal model delta sigma weight residual 1.537 1.544 -0.007 5.00e-03 4.00e+04 2.05e+00 bond pdb=" CA VAL F 87 " pdb=" C VAL F 87 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.05e-02 9.07e+03 2.00e+00 ... (remaining 19639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 25639 2.02 - 4.04: 774 4.04 - 6.05: 144 6.05 - 8.07: 35 8.07 - 10.09: 24 Bond angle restraints: 26616 Sorted by residual: angle pdb=" N VAL B 87 " pdb=" CA VAL B 87 " pdb=" C VAL B 87 " ideal model delta sigma weight residual 108.88 117.40 -8.52 2.16e+00 2.14e-01 1.56e+01 angle pdb=" N VAL F 87 " pdb=" CA VAL F 87 " pdb=" C VAL F 87 " ideal model delta sigma weight residual 108.88 117.38 -8.50 2.16e+00 2.14e-01 1.55e+01 angle pdb=" N VAL E 87 " pdb=" CA VAL E 87 " pdb=" C VAL E 87 " ideal model delta sigma weight residual 108.88 117.37 -8.49 2.16e+00 2.14e-01 1.54e+01 angle pdb=" N VAL D 87 " pdb=" CA VAL D 87 " pdb=" C VAL D 87 " ideal model delta sigma weight residual 108.88 117.36 -8.48 2.16e+00 2.14e-01 1.54e+01 angle pdb=" N VAL A 87 " pdb=" CA VAL A 87 " pdb=" C VAL A 87 " ideal model delta sigma weight residual 108.88 117.36 -8.48 2.16e+00 2.14e-01 1.54e+01 ... (remaining 26611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 9768 14.70 - 29.41: 1218 29.41 - 44.11: 426 44.11 - 58.82: 48 58.82 - 73.52: 12 Dihedral angle restraints: 11472 sinusoidal: 4596 harmonic: 6876 Sorted by residual: dihedral pdb=" CA PRO C 193 " pdb=" C PRO C 193 " pdb=" N HIS C 194 " pdb=" CA HIS C 194 " ideal model delta harmonic sigma weight residual -180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PRO E 193 " pdb=" C PRO E 193 " pdb=" N HIS E 194 " pdb=" CA HIS E 194 " ideal model delta harmonic sigma weight residual 180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PRO B 193 " pdb=" C PRO B 193 " pdb=" N HIS B 194 " pdb=" CA HIS B 194 " ideal model delta harmonic sigma weight residual -180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 11469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1816 0.037 - 0.073: 869 0.073 - 0.110: 270 0.110 - 0.146: 60 0.146 - 0.183: 9 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CB ILE G 156 " pdb=" CA ILE G 156 " pdb=" CG1 ILE G 156 " pdb=" CG2 ILE G 156 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CB ILE L 156 " pdb=" CA ILE L 156 " pdb=" CG1 ILE L 156 " pdb=" CG2 ILE L 156 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CB ILE I 156 " pdb=" CA ILE I 156 " pdb=" CG1 ILE I 156 " pdb=" CG2 ILE I 156 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.97e-01 ... (remaining 3021 not shown) Planarity restraints: 3204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 105 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C LYS J 105 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS J 105 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU J 106 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 105 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C LYS G 105 " -0.041 2.00e-02 2.50e+03 pdb=" O LYS G 105 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU G 106 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 105 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.64e+00 pdb=" C LYS K 105 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS K 105 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU K 106 " -0.014 2.00e-02 2.50e+03 ... (remaining 3201 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5167 2.79 - 3.32: 16736 3.32 - 3.85: 30244 3.85 - 4.37: 31957 4.37 - 4.90: 57178 Nonbonded interactions: 141282 Sorted by model distance: nonbonded pdb=" O PRO E 203 " pdb=" OG1 THR E 207 " model vdw 2.268 3.040 nonbonded pdb=" O PRO B 203 " pdb=" OG1 THR B 207 " model vdw 2.269 3.040 nonbonded pdb=" O PRO A 203 " pdb=" OG1 THR A 207 " model vdw 2.269 3.040 nonbonded pdb=" O PRO D 203 " pdb=" OG1 THR D 207 " model vdw 2.269 3.040 nonbonded pdb=" O PRO F 203 " pdb=" OG1 THR F 207 " model vdw 2.269 3.040 ... (remaining 141277 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.630 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 19680 Z= 0.274 Angle : 0.921 10.088 26688 Z= 0.510 Chirality : 0.046 0.183 3024 Planarity : 0.006 0.049 3204 Dihedral : 14.356 73.522 6924 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.57 % Allowed : 7.90 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.14), residues: 2304 helix: -1.87 (0.10), residues: 1536 sheet: -0.74 (0.41), residues: 174 loop : -2.99 (0.21), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 53 TYR 0.012 0.002 TYR F 155 PHE 0.014 0.002 PHE D 161 TRP 0.009 0.001 TRP A 4 HIS 0.002 0.001 HIS K 95 Details of bonding type rmsd covalent geometry : bond 0.00596 (19644) covalent geometry : angle 0.92188 (26616) SS BOND : bond 0.00268 ( 36) SS BOND : angle 0.62449 ( 72) hydrogen bonds : bond 0.21863 ( 1200) hydrogen bonds : angle 6.14453 ( 3564) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 559 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8860 (tt) cc_final: 0.8401 (mm) REVERT: A 155 TYR cc_start: 0.8972 (t80) cc_final: 0.8700 (t80) REVERT: A 157 ILE cc_start: 0.9323 (mt) cc_final: 0.9072 (mt) REVERT: G 47 ASP cc_start: 0.8712 (p0) cc_final: 0.8441 (p0) REVERT: G 92 TYR cc_start: 0.8894 (t80) cc_final: 0.8379 (t80) REVERT: B 17 TYR cc_start: 0.6498 (m-80) cc_final: 0.6296 (m-80) REVERT: B 90 LEU cc_start: 0.8813 (tt) cc_final: 0.8383 (mm) REVERT: B 155 TYR cc_start: 0.8968 (t80) cc_final: 0.8692 (t80) REVERT: B 157 ILE cc_start: 0.9394 (mt) cc_final: 0.9128 (mt) REVERT: L 47 ASP cc_start: 0.8551 (p0) cc_final: 0.8098 (p0) REVERT: L 92 TYR cc_start: 0.8840 (t80) cc_final: 0.8394 (t80) REVERT: C 90 LEU cc_start: 0.8812 (tt) cc_final: 0.8408 (mm) REVERT: C 153 ARG cc_start: 0.8957 (mtt180) cc_final: 0.8580 (mmt180) REVERT: C 157 ILE cc_start: 0.9390 (mt) cc_final: 0.9126 (mt) REVERT: C 212 PHE cc_start: 0.8398 (t80) cc_final: 0.8086 (t80) REVERT: K 47 ASP cc_start: 0.8564 (p0) cc_final: 0.8305 (p0) REVERT: K 92 TYR cc_start: 0.8843 (t80) cc_final: 0.8434 (t80) REVERT: D 90 LEU cc_start: 0.8865 (tt) cc_final: 0.8406 (mm) REVERT: D 155 TYR cc_start: 0.8974 (t80) cc_final: 0.8699 (t80) REVERT: D 157 ILE cc_start: 0.9321 (mt) cc_final: 0.9072 (mt) REVERT: J 47 ASP cc_start: 0.8589 (p0) cc_final: 0.8135 (p0) REVERT: J 92 TYR cc_start: 0.8884 (t80) cc_final: 0.8420 (t80) REVERT: E 17 TYR cc_start: 0.6482 (m-80) cc_final: 0.6277 (m-80) REVERT: E 48 GLU cc_start: 0.8585 (pt0) cc_final: 0.8332 (pt0) REVERT: E 90 LEU cc_start: 0.8825 (tt) cc_final: 0.8395 (mm) REVERT: E 155 TYR cc_start: 0.9013 (t80) cc_final: 0.8777 (t80) REVERT: E 157 ILE cc_start: 0.9374 (mt) cc_final: 0.9109 (mt) REVERT: E 212 PHE cc_start: 0.8310 (t80) cc_final: 0.7998 (t80) REVERT: I 47 ASP cc_start: 0.8568 (p0) cc_final: 0.8112 (p0) REVERT: I 92 TYR cc_start: 0.8842 (t80) cc_final: 0.8391 (t80) REVERT: F 90 LEU cc_start: 0.8807 (tt) cc_final: 0.8405 (mm) REVERT: F 153 ARG cc_start: 0.8947 (mtt180) cc_final: 0.8571 (mmt180) REVERT: F 157 ILE cc_start: 0.9388 (mt) cc_final: 0.9118 (mt) REVERT: F 202 ARG cc_start: 0.8968 (mtt180) cc_final: 0.8680 (mtt-85) REVERT: F 212 PHE cc_start: 0.8412 (t80) cc_final: 0.8098 (t80) REVERT: H 92 TYR cc_start: 0.8853 (t80) cc_final: 0.8382 (t80) REVERT: H 98 TYR cc_start: 0.9196 (m-80) cc_final: 0.8975 (m-80) outliers start: 12 outliers final: 12 residues processed: 565 average time/residue: 0.1550 time to fit residues: 129.7881 Evaluate side-chains 455 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 443 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain H residue 156 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0770 chunk 200 optimal weight: 7.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN G 49 GLN B 224 ASN L 49 GLN C 224 ASN K 49 GLN D 224 ASN J 49 GLN E 224 ASN I 49 GLN F 224 ASN H 49 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.108298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.080358 restraints weight = 44036.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.082445 restraints weight = 20679.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.083693 restraints weight = 13116.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.084363 restraints weight = 10237.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.084557 restraints weight = 9040.424| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19680 Z= 0.122 Angle : 0.614 9.678 26688 Z= 0.305 Chirality : 0.036 0.119 3024 Planarity : 0.004 0.042 3204 Dihedral : 5.084 46.015 2550 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.00 % Allowed : 13.76 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.16), residues: 2304 helix: 0.34 (0.11), residues: 1608 sheet: -0.16 (0.39), residues: 174 loop : -2.73 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 53 TYR 0.018 0.001 TYR D 230 PHE 0.013 0.001 PHE L 232 TRP 0.007 0.001 TRP B 4 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00250 (19644) covalent geometry : angle 0.61430 (26616) SS BOND : bond 0.00083 ( 36) SS BOND : angle 0.65246 ( 72) hydrogen bonds : bond 0.05169 ( 1200) hydrogen bonds : angle 3.60180 ( 3564) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 482 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8902 (tt) cc_final: 0.8422 (mm) REVERT: A 104 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8354 (mm-30) REVERT: A 155 TYR cc_start: 0.9011 (t80) cc_final: 0.8577 (t80) REVERT: A 161 PHE cc_start: 0.9051 (m-80) cc_final: 0.8617 (m-80) REVERT: G 92 TYR cc_start: 0.8796 (t80) cc_final: 0.8346 (t80) REVERT: G 104 GLU cc_start: 0.7091 (tp30) cc_final: 0.6807 (tp30) REVERT: G 212 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8480 (t80) REVERT: B 92 TYR cc_start: 0.8782 (t80) cc_final: 0.8566 (t80) REVERT: B 155 TYR cc_start: 0.8996 (t80) cc_final: 0.8592 (t80) REVERT: B 161 PHE cc_start: 0.9098 (m-80) cc_final: 0.8631 (m-80) REVERT: L 47 ASP cc_start: 0.8394 (p0) cc_final: 0.8054 (p0) REVERT: L 92 TYR cc_start: 0.8742 (t80) cc_final: 0.8493 (t80) REVERT: L 212 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8354 (t80) REVERT: C 90 LEU cc_start: 0.8893 (tt) cc_final: 0.8414 (mm) REVERT: C 104 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8213 (mt-10) REVERT: C 153 ARG cc_start: 0.8926 (mtt180) cc_final: 0.8591 (mmt180) REVERT: C 161 PHE cc_start: 0.9057 (m-80) cc_final: 0.8616 (m-80) REVERT: C 212 PHE cc_start: 0.8307 (t80) cc_final: 0.8089 (t80) REVERT: K 47 ASP cc_start: 0.8351 (p0) cc_final: 0.8048 (p0) REVERT: K 92 TYR cc_start: 0.8720 (t80) cc_final: 0.8344 (t80) REVERT: K 212 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8415 (t80) REVERT: D 90 LEU cc_start: 0.8907 (tt) cc_final: 0.8427 (mm) REVERT: D 104 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8354 (mm-30) REVERT: D 155 TYR cc_start: 0.9015 (t80) cc_final: 0.8583 (t80) REVERT: D 161 PHE cc_start: 0.9047 (m-80) cc_final: 0.8612 (m-80) REVERT: J 92 TYR cc_start: 0.8770 (t80) cc_final: 0.8374 (t80) REVERT: J 212 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8450 (t80) REVERT: E 48 GLU cc_start: 0.8631 (pt0) cc_final: 0.8343 (pt0) REVERT: E 155 TYR cc_start: 0.9026 (t80) cc_final: 0.8702 (t80) REVERT: E 161 PHE cc_start: 0.9092 (m-80) cc_final: 0.8623 (m-80) REVERT: E 212 PHE cc_start: 0.8243 (t80) cc_final: 0.8036 (t80) REVERT: I 92 TYR cc_start: 0.8730 (t80) cc_final: 0.8483 (t80) REVERT: I 212 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8363 (t80) REVERT: F 90 LEU cc_start: 0.8903 (tt) cc_final: 0.8421 (mm) REVERT: F 104 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8314 (mm-30) REVERT: F 107 ASN cc_start: 0.7367 (t0) cc_final: 0.7103 (t0) REVERT: F 153 ARG cc_start: 0.8929 (mtt180) cc_final: 0.8590 (mmt180) REVERT: F 161 PHE cc_start: 0.9055 (m-80) cc_final: 0.8612 (m-80) REVERT: F 202 ARG cc_start: 0.8992 (mtt180) cc_final: 0.8770 (mtt180) REVERT: F 212 PHE cc_start: 0.8303 (t80) cc_final: 0.8053 (t80) REVERT: F 213 MET cc_start: 0.8924 (mmm) cc_final: 0.8583 (mmm) REVERT: H 47 ASP cc_start: 0.8381 (p0) cc_final: 0.8152 (p0) REVERT: H 92 TYR cc_start: 0.8755 (t80) cc_final: 0.8330 (t80) REVERT: H 212 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8488 (t80) outliers start: 42 outliers final: 24 residues processed: 506 average time/residue: 0.1278 time to fit residues: 101.2960 Evaluate side-chains 472 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 442 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 212 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 27 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 95 optimal weight: 0.0270 chunk 2 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 179 optimal weight: 0.0970 chunk 99 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 overall best weight: 0.9038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.109571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.081494 restraints weight = 44383.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.083561 restraints weight = 20983.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.084796 restraints weight = 13497.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.085457 restraints weight = 10600.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.085817 restraints weight = 9364.997| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19680 Z= 0.110 Angle : 0.616 12.009 26688 Z= 0.291 Chirality : 0.036 0.119 3024 Planarity : 0.003 0.045 3204 Dihedral : 4.371 33.039 2544 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.52 % Allowed : 17.62 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.17), residues: 2304 helix: 1.33 (0.12), residues: 1608 sheet: 0.12 (0.40), residues: 174 loop : -2.49 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 53 TYR 0.016 0.001 TYR K 230 PHE 0.029 0.001 PHE H 32 TRP 0.011 0.001 TRP C 25 HIS 0.004 0.000 HIS H 95 Details of bonding type rmsd covalent geometry : bond 0.00227 (19644) covalent geometry : angle 0.61636 (26616) SS BOND : bond 0.00073 ( 36) SS BOND : angle 0.52240 ( 72) hydrogen bonds : bond 0.04270 ( 1200) hydrogen bonds : angle 3.32265 ( 3564) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 454 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8293 (mt-10) REVERT: A 161 PHE cc_start: 0.9054 (m-80) cc_final: 0.8618 (m-80) REVERT: G 28 VAL cc_start: 0.9422 (t) cc_final: 0.9190 (m) REVERT: G 104 GLU cc_start: 0.7178 (tp30) cc_final: 0.6846 (tp30) REVERT: G 212 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8405 (t80) REVERT: B 161 PHE cc_start: 0.9112 (m-80) cc_final: 0.8646 (m-80) REVERT: L 47 ASP cc_start: 0.8365 (p0) cc_final: 0.8025 (p0) REVERT: L 92 TYR cc_start: 0.8663 (t80) cc_final: 0.8457 (t80) REVERT: L 212 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8314 (t80) REVERT: C 153 ARG cc_start: 0.8882 (mtt180) cc_final: 0.8575 (mmt180) REVERT: C 161 PHE cc_start: 0.9070 (m-80) cc_final: 0.8642 (m-80) REVERT: C 212 PHE cc_start: 0.8264 (t80) cc_final: 0.8031 (t80) REVERT: K 47 ASP cc_start: 0.8319 (p0) cc_final: 0.8014 (p0) REVERT: K 92 TYR cc_start: 0.8640 (t80) cc_final: 0.8175 (t80) REVERT: K 212 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8381 (t80) REVERT: D 104 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8295 (mt-10) REVERT: D 161 PHE cc_start: 0.9053 (m-80) cc_final: 0.8615 (m-80) REVERT: J 28 VAL cc_start: 0.9461 (t) cc_final: 0.9219 (m) REVERT: J 212 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8374 (t80) REVERT: E 48 GLU cc_start: 0.8569 (pt0) cc_final: 0.8358 (pt0) REVERT: E 161 PHE cc_start: 0.9104 (m-80) cc_final: 0.8673 (m-80) REVERT: E 212 PHE cc_start: 0.8216 (t80) cc_final: 0.7992 (t80) REVERT: I 47 ASP cc_start: 0.8284 (p0) cc_final: 0.8033 (p0) REVERT: I 92 TYR cc_start: 0.8675 (t80) cc_final: 0.8441 (t80) REVERT: I 212 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8327 (t80) REVERT: F 153 ARG cc_start: 0.8875 (mtt180) cc_final: 0.8574 (mmt180) REVERT: F 161 PHE cc_start: 0.9062 (m-80) cc_final: 0.8630 (m-80) REVERT: F 202 ARG cc_start: 0.8991 (mtt180) cc_final: 0.8765 (mtt180) REVERT: F 212 PHE cc_start: 0.8273 (t80) cc_final: 0.8042 (t80) REVERT: H 47 ASP cc_start: 0.8365 (p0) cc_final: 0.8121 (p0) REVERT: H 92 TYR cc_start: 0.8696 (t80) cc_final: 0.8278 (t80) REVERT: H 212 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8455 (t80) outliers start: 53 outliers final: 37 residues processed: 492 average time/residue: 0.1175 time to fit residues: 91.1717 Evaluate side-chains 472 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 429 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 97 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 34 optimal weight: 30.0000 chunk 107 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.079676 restraints weight = 44972.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.081749 restraints weight = 20766.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.082960 restraints weight = 13306.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.083622 restraints weight = 10499.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.083955 restraints weight = 9307.886| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19680 Z= 0.168 Angle : 0.637 11.678 26688 Z= 0.310 Chirality : 0.037 0.117 3024 Planarity : 0.004 0.044 3204 Dihedral : 4.149 22.704 2544 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.81 % Allowed : 18.24 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2304 helix: 1.74 (0.12), residues: 1578 sheet: 0.25 (0.40), residues: 174 loop : -2.03 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 202 TYR 0.017 0.002 TYR A 230 PHE 0.018 0.001 PHE G 97 TRP 0.014 0.001 TRP B 25 HIS 0.010 0.001 HIS H 95 Details of bonding type rmsd covalent geometry : bond 0.00382 (19644) covalent geometry : angle 0.63696 (26616) SS BOND : bond 0.00198 ( 36) SS BOND : angle 0.48514 ( 72) hydrogen bonds : bond 0.04367 ( 1200) hydrogen bonds : angle 3.43041 ( 3564) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 442 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8619 (pt0) cc_final: 0.8342 (pt0) REVERT: A 100 MET cc_start: 0.8747 (ttp) cc_final: 0.8499 (tmm) REVERT: A 161 PHE cc_start: 0.9118 (m-80) cc_final: 0.8739 (m-80) REVERT: G 28 VAL cc_start: 0.9431 (t) cc_final: 0.9207 (m) REVERT: G 104 GLU cc_start: 0.7362 (tp30) cc_final: 0.6990 (tp30) REVERT: G 212 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8435 (t80) REVERT: B 161 PHE cc_start: 0.9157 (m-80) cc_final: 0.8676 (m-80) REVERT: L 47 ASP cc_start: 0.8446 (p0) cc_final: 0.8137 (p0) REVERT: L 92 TYR cc_start: 0.8742 (t80) cc_final: 0.8487 (t80) REVERT: L 212 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8333 (t80) REVERT: C 153 ARG cc_start: 0.8922 (mtt180) cc_final: 0.8618 (mmt180) REVERT: C 161 PHE cc_start: 0.9126 (m-80) cc_final: 0.8663 (m-80) REVERT: C 212 PHE cc_start: 0.8345 (t80) cc_final: 0.8093 (t80) REVERT: K 47 ASP cc_start: 0.8414 (p0) cc_final: 0.8132 (p0) REVERT: K 92 TYR cc_start: 0.8704 (t80) cc_final: 0.8156 (t80) REVERT: K 212 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8449 (t80) REVERT: D 100 MET cc_start: 0.8745 (ttp) cc_final: 0.8499 (tmm) REVERT: D 161 PHE cc_start: 0.9111 (m-80) cc_final: 0.8734 (m-80) REVERT: J 28 VAL cc_start: 0.9480 (t) cc_final: 0.9255 (m) REVERT: J 212 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8416 (t80) REVERT: E 48 GLU cc_start: 0.8630 (pt0) cc_final: 0.8391 (pt0) REVERT: E 161 PHE cc_start: 0.9206 (m-80) cc_final: 0.8728 (m-80) REVERT: E 212 PHE cc_start: 0.8310 (t80) cc_final: 0.8055 (t80) REVERT: I 47 ASP cc_start: 0.8383 (p0) cc_final: 0.8134 (p0) REVERT: I 92 TYR cc_start: 0.8767 (t80) cc_final: 0.8476 (t80) REVERT: I 212 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8348 (t80) REVERT: F 104 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8413 (mt-10) REVERT: F 161 PHE cc_start: 0.9121 (m-80) cc_final: 0.8632 (m-80) REVERT: F 202 ARG cc_start: 0.9024 (mtt180) cc_final: 0.8756 (mtt180) REVERT: F 212 PHE cc_start: 0.8336 (t80) cc_final: 0.8085 (t80) REVERT: H 47 ASP cc_start: 0.8423 (p0) cc_final: 0.8165 (p0) REVERT: H 92 TYR cc_start: 0.8714 (t80) cc_final: 0.8258 (t80) REVERT: H 212 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8493 (t80) outliers start: 59 outliers final: 47 residues processed: 477 average time/residue: 0.1221 time to fit residues: 93.2320 Evaluate side-chains 483 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 430 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 69 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 219 optimal weight: 0.5980 chunk 198 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95 HIS J 95 HIS H 95 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.108824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.081087 restraints weight = 44223.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.083112 restraints weight = 20558.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.084289 restraints weight = 13275.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.084921 restraints weight = 10482.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.085260 restraints weight = 9330.917| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19680 Z= 0.119 Angle : 0.624 11.274 26688 Z= 0.294 Chirality : 0.036 0.111 3024 Planarity : 0.003 0.043 3204 Dihedral : 3.969 16.305 2542 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.81 % Allowed : 19.67 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.17), residues: 2304 helix: 2.00 (0.13), residues: 1578 sheet: 0.41 (0.41), residues: 174 loop : -1.99 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 101 TYR 0.017 0.001 TYR I 230 PHE 0.029 0.001 PHE H 32 TRP 0.016 0.001 TRP D 25 HIS 0.008 0.001 HIS H 95 Details of bonding type rmsd covalent geometry : bond 0.00262 (19644) covalent geometry : angle 0.62417 (26616) SS BOND : bond 0.00130 ( 36) SS BOND : angle 0.49971 ( 72) hydrogen bonds : bond 0.04018 ( 1200) hydrogen bonds : angle 3.25888 ( 3564) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 450 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8957 (tt) cc_final: 0.8337 (mm) REVERT: A 100 MET cc_start: 0.8730 (ttp) cc_final: 0.8505 (tmm) REVERT: A 157 ILE cc_start: 0.9549 (pt) cc_final: 0.9216 (mt) REVERT: A 161 PHE cc_start: 0.9116 (m-80) cc_final: 0.8583 (m-80) REVERT: G 28 VAL cc_start: 0.9413 (t) cc_final: 0.9193 (m) REVERT: G 156 ILE cc_start: 0.9252 (pt) cc_final: 0.9034 (mm) REVERT: G 212 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8406 (t80) REVERT: B 90 LEU cc_start: 0.8944 (tt) cc_final: 0.8345 (mm) REVERT: B 161 PHE cc_start: 0.9133 (m-80) cc_final: 0.8643 (m-80) REVERT: L 47 ASP cc_start: 0.8428 (p0) cc_final: 0.8098 (p0) REVERT: L 92 TYR cc_start: 0.8723 (t80) cc_final: 0.8449 (t80) REVERT: L 212 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8316 (t80) REVERT: C 90 LEU cc_start: 0.8940 (tt) cc_final: 0.8350 (mm) REVERT: C 161 PHE cc_start: 0.9097 (m-80) cc_final: 0.8617 (m-80) REVERT: K 47 ASP cc_start: 0.8394 (p0) cc_final: 0.8102 (p0) REVERT: K 92 TYR cc_start: 0.8704 (t80) cc_final: 0.8163 (t80) REVERT: K 212 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8393 (t80) REVERT: D 90 LEU cc_start: 0.8962 (tt) cc_final: 0.8345 (mm) REVERT: D 100 MET cc_start: 0.8728 (ttp) cc_final: 0.8502 (tmm) REVERT: D 157 ILE cc_start: 0.9547 (pt) cc_final: 0.9213 (mt) REVERT: D 161 PHE cc_start: 0.9106 (m-80) cc_final: 0.8575 (m-80) REVERT: J 28 VAL cc_start: 0.9467 (t) cc_final: 0.9247 (m) REVERT: J 212 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8360 (t80) REVERT: E 48 GLU cc_start: 0.8597 (pt0) cc_final: 0.8348 (pt0) REVERT: E 90 LEU cc_start: 0.8951 (tt) cc_final: 0.8346 (mm) REVERT: E 161 PHE cc_start: 0.9188 (m-80) cc_final: 0.8695 (m-80) REVERT: E 212 PHE cc_start: 0.8281 (t80) cc_final: 0.8053 (t80) REVERT: I 47 ASP cc_start: 0.8346 (p0) cc_final: 0.8073 (p0) REVERT: I 92 TYR cc_start: 0.8733 (t80) cc_final: 0.8466 (t80) REVERT: I 212 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8301 (t80) REVERT: F 90 LEU cc_start: 0.8941 (tt) cc_final: 0.8351 (mm) REVERT: F 100 MET cc_start: 0.8727 (ttp) cc_final: 0.8475 (tmm) REVERT: F 157 ILE cc_start: 0.9525 (mt) cc_final: 0.9227 (pt) REVERT: F 161 PHE cc_start: 0.9091 (m-80) cc_final: 0.8687 (m-80) REVERT: F 202 ARG cc_start: 0.8995 (mtt180) cc_final: 0.8738 (mtt180) REVERT: F 212 PHE cc_start: 0.8305 (t80) cc_final: 0.8072 (t80) REVERT: H 47 ASP cc_start: 0.8393 (p0) cc_final: 0.8143 (p0) REVERT: H 92 TYR cc_start: 0.8712 (t80) cc_final: 0.8235 (t80) REVERT: H 212 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8470 (t80) outliers start: 59 outliers final: 43 residues processed: 485 average time/residue: 0.1209 time to fit residues: 94.5257 Evaluate side-chains 473 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 424 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.107210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.079075 restraints weight = 44412.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.081039 restraints weight = 20987.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.082146 restraints weight = 13747.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.082743 restraints weight = 10989.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.083040 restraints weight = 9845.253| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19680 Z= 0.201 Angle : 0.648 10.900 26688 Z= 0.319 Chirality : 0.038 0.118 3024 Planarity : 0.004 0.043 3204 Dihedral : 3.993 16.716 2532 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.67 % Allowed : 20.00 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.17), residues: 2304 helix: 2.03 (0.12), residues: 1572 sheet: 0.27 (0.40), residues: 174 loop : -1.63 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 76 TYR 0.019 0.002 TYR I 230 PHE 0.023 0.001 PHE I 32 TRP 0.014 0.001 TRP F 25 HIS 0.010 0.001 HIS H 95 Details of bonding type rmsd covalent geometry : bond 0.00461 (19644) covalent geometry : angle 0.64843 (26616) SS BOND : bond 0.00228 ( 36) SS BOND : angle 0.49951 ( 72) hydrogen bonds : bond 0.04483 ( 1200) hydrogen bonds : angle 3.49939 ( 3564) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 429 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8727 (ttp) cc_final: 0.8454 (tmm) REVERT: A 161 PHE cc_start: 0.9120 (m-80) cc_final: 0.8622 (m-80) REVERT: G 28 VAL cc_start: 0.9441 (t) cc_final: 0.9239 (m) REVERT: G 156 ILE cc_start: 0.9256 (pt) cc_final: 0.9054 (mm) REVERT: G 212 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8441 (t80) REVERT: B 155 TYR cc_start: 0.8970 (t80) cc_final: 0.8612 (t80) REVERT: B 161 PHE cc_start: 0.9145 (m-80) cc_final: 0.8650 (m-80) REVERT: L 47 ASP cc_start: 0.8461 (p0) cc_final: 0.8153 (p0) REVERT: L 92 TYR cc_start: 0.8823 (t80) cc_final: 0.8534 (t80) REVERT: L 212 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8314 (t80) REVERT: C 100 MET cc_start: 0.8699 (ttp) cc_final: 0.8498 (tmm) REVERT: C 157 ILE cc_start: 0.9531 (mt) cc_final: 0.9225 (pt) REVERT: C 161 PHE cc_start: 0.9107 (m-80) cc_final: 0.8691 (m-80) REVERT: K 47 ASP cc_start: 0.8407 (p0) cc_final: 0.8149 (p0) REVERT: K 92 TYR cc_start: 0.8793 (t80) cc_final: 0.8251 (t80) REVERT: K 212 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8471 (t80) REVERT: D 100 MET cc_start: 0.8725 (ttp) cc_final: 0.8455 (tmm) REVERT: D 157 ILE cc_start: 0.9514 (pt) cc_final: 0.9313 (mt) REVERT: D 161 PHE cc_start: 0.9116 (m-80) cc_final: 0.8617 (m-80) REVERT: J 28 VAL cc_start: 0.9485 (t) cc_final: 0.9269 (m) REVERT: J 212 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8433 (t80) REVERT: E 48 GLU cc_start: 0.8564 (pt0) cc_final: 0.8356 (pt0) REVERT: E 161 PHE cc_start: 0.9202 (m-80) cc_final: 0.8718 (m-80) REVERT: I 47 ASP cc_start: 0.8394 (p0) cc_final: 0.8151 (p0) REVERT: I 92 TYR cc_start: 0.8848 (t80) cc_final: 0.8503 (t80) REVERT: I 212 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8317 (t80) REVERT: F 100 MET cc_start: 0.8729 (ttp) cc_final: 0.8487 (tmm) REVERT: F 157 ILE cc_start: 0.9528 (mt) cc_final: 0.9224 (pt) REVERT: F 161 PHE cc_start: 0.9108 (m-80) cc_final: 0.8690 (m-80) REVERT: F 202 ARG cc_start: 0.9011 (mtt180) cc_final: 0.8758 (mtt180) REVERT: F 212 PHE cc_start: 0.8339 (t80) cc_final: 0.8093 (t80) REVERT: H 47 ASP cc_start: 0.8400 (p0) cc_final: 0.8152 (p0) REVERT: H 92 TYR cc_start: 0.8796 (t80) cc_final: 0.8291 (t80) REVERT: H 212 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8514 (t80) REVERT: H 230 TYR cc_start: 0.8215 (t80) cc_final: 0.7797 (t80) outliers start: 77 outliers final: 55 residues processed: 474 average time/residue: 0.1217 time to fit residues: 93.2806 Evaluate side-chains 479 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 418 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 123 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.108074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.079835 restraints weight = 44436.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.081823 restraints weight = 21207.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.083007 restraints weight = 13678.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.083634 restraints weight = 10836.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.083825 restraints weight = 9655.857| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19680 Z= 0.148 Angle : 0.651 12.294 26688 Z= 0.309 Chirality : 0.036 0.112 3024 Planarity : 0.003 0.044 3204 Dihedral : 3.977 18.198 2532 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.33 % Allowed : 20.86 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.17), residues: 2304 helix: 2.14 (0.12), residues: 1572 sheet: 0.37 (0.41), residues: 174 loop : -1.58 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 76 TYR 0.018 0.001 TYR D 230 PHE 0.031 0.001 PHE K 32 TRP 0.016 0.001 TRP B 25 HIS 0.002 0.000 HIS H 95 Details of bonding type rmsd covalent geometry : bond 0.00338 (19644) covalent geometry : angle 0.65115 (26616) SS BOND : bond 0.00169 ( 36) SS BOND : angle 0.53618 ( 72) hydrogen bonds : bond 0.04276 ( 1200) hydrogen bonds : angle 3.38690 ( 3564) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 434 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8728 (ttp) cc_final: 0.8480 (tmm) REVERT: A 155 TYR cc_start: 0.8972 (t80) cc_final: 0.8676 (t80) REVERT: A 161 PHE cc_start: 0.9123 (m-80) cc_final: 0.8652 (m-80) REVERT: G 28 VAL cc_start: 0.9428 (t) cc_final: 0.9214 (m) REVERT: G 212 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8430 (t80) REVERT: B 155 TYR cc_start: 0.8952 (t80) cc_final: 0.8600 (t80) REVERT: B 161 PHE cc_start: 0.9165 (m-80) cc_final: 0.8654 (m-80) REVERT: L 47 ASP cc_start: 0.8460 (p0) cc_final: 0.8146 (p0) REVERT: L 92 TYR cc_start: 0.8803 (t80) cc_final: 0.8531 (t80) REVERT: L 212 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8312 (t80) REVERT: C 100 MET cc_start: 0.8719 (ttp) cc_final: 0.8498 (tmm) REVERT: C 157 ILE cc_start: 0.9537 (mt) cc_final: 0.9226 (pt) REVERT: C 161 PHE cc_start: 0.9123 (m-80) cc_final: 0.8696 (m-80) REVERT: K 47 ASP cc_start: 0.8413 (p0) cc_final: 0.8163 (p0) REVERT: K 92 TYR cc_start: 0.8779 (t80) cc_final: 0.8264 (t80) REVERT: K 212 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8450 (t80) REVERT: D 100 MET cc_start: 0.8726 (ttp) cc_final: 0.8480 (tmm) REVERT: D 155 TYR cc_start: 0.8954 (t80) cc_final: 0.8640 (t80) REVERT: D 157 ILE cc_start: 0.9518 (pt) cc_final: 0.9316 (mt) REVERT: D 161 PHE cc_start: 0.9145 (m-80) cc_final: 0.8648 (m-80) REVERT: J 28 VAL cc_start: 0.9477 (t) cc_final: 0.9263 (m) REVERT: J 212 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8416 (t80) REVERT: E 48 GLU cc_start: 0.8559 (pt0) cc_final: 0.8335 (pt0) REVERT: E 161 PHE cc_start: 0.9220 (m-80) cc_final: 0.8729 (m-80) REVERT: I 47 ASP cc_start: 0.8384 (p0) cc_final: 0.8105 (p0) REVERT: I 92 TYR cc_start: 0.8828 (t80) cc_final: 0.8478 (t80) REVERT: I 212 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8317 (t80) REVERT: F 100 MET cc_start: 0.8696 (ttp) cc_final: 0.8483 (tmm) REVERT: F 157 ILE cc_start: 0.9538 (mt) cc_final: 0.9228 (pt) REVERT: F 161 PHE cc_start: 0.9129 (m-80) cc_final: 0.8698 (m-80) REVERT: F 202 ARG cc_start: 0.8989 (mtt180) cc_final: 0.8724 (mtt180) REVERT: F 212 PHE cc_start: 0.8347 (t80) cc_final: 0.8144 (t80) REVERT: H 47 ASP cc_start: 0.8397 (p0) cc_final: 0.8150 (p0) REVERT: H 92 TYR cc_start: 0.8754 (t80) cc_final: 0.8219 (t80) REVERT: H 212 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8492 (t80) REVERT: H 230 TYR cc_start: 0.8217 (t80) cc_final: 0.7807 (t80) outliers start: 70 outliers final: 57 residues processed: 467 average time/residue: 0.1234 time to fit residues: 92.9985 Evaluate side-chains 481 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 418 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 159 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.107177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.079065 restraints weight = 44982.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.081094 restraints weight = 20638.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082273 restraints weight = 13237.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.082942 restraints weight = 10483.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.083107 restraints weight = 9295.904| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19680 Z= 0.201 Angle : 0.676 12.150 26688 Z= 0.329 Chirality : 0.038 0.129 3024 Planarity : 0.004 0.044 3204 Dihedral : 4.027 17.477 2532 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.52 % Allowed : 20.81 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.17), residues: 2304 helix: 2.11 (0.12), residues: 1572 sheet: 0.24 (0.40), residues: 174 loop : -1.37 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 76 TYR 0.024 0.002 TYR I 230 PHE 0.016 0.001 PHE K 97 TRP 0.015 0.001 TRP B 25 HIS 0.008 0.001 HIS H 95 Details of bonding type rmsd covalent geometry : bond 0.00463 (19644) covalent geometry : angle 0.67655 (26616) SS BOND : bond 0.00231 ( 36) SS BOND : angle 0.51053 ( 72) hydrogen bonds : bond 0.04567 ( 1200) hydrogen bonds : angle 3.55540 ( 3564) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 418 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8720 (ttp) cc_final: 0.8464 (tmm) REVERT: A 161 PHE cc_start: 0.9170 (m-80) cc_final: 0.8685 (m-80) REVERT: G 28 VAL cc_start: 0.9427 (t) cc_final: 0.9226 (m) REVERT: G 212 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8480 (t80) REVERT: B 155 TYR cc_start: 0.8996 (t80) cc_final: 0.8703 (t80) REVERT: B 161 PHE cc_start: 0.9194 (m-80) cc_final: 0.8690 (m-80) REVERT: L 47 ASP cc_start: 0.8539 (p0) cc_final: 0.8240 (p0) REVERT: L 92 TYR cc_start: 0.8843 (t80) cc_final: 0.8526 (t80) REVERT: L 212 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8355 (t80) REVERT: C 100 MET cc_start: 0.8712 (ttp) cc_final: 0.8483 (tmm) REVERT: C 157 ILE cc_start: 0.9543 (mt) cc_final: 0.9242 (pt) REVERT: C 161 PHE cc_start: 0.9142 (m-80) cc_final: 0.8691 (m-80) REVERT: K 47 ASP cc_start: 0.8497 (p0) cc_final: 0.8242 (p0) REVERT: K 92 TYR cc_start: 0.8798 (t80) cc_final: 0.8260 (t80) REVERT: K 212 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8530 (t80) REVERT: D 100 MET cc_start: 0.8718 (ttp) cc_final: 0.8468 (tmm) REVERT: D 155 TYR cc_start: 0.8987 (t80) cc_final: 0.8701 (t80) REVERT: D 161 PHE cc_start: 0.9185 (m-80) cc_final: 0.8693 (m-80) REVERT: J 28 VAL cc_start: 0.9480 (t) cc_final: 0.9274 (m) REVERT: J 212 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8466 (t80) REVERT: E 48 GLU cc_start: 0.8598 (pt0) cc_final: 0.8378 (pt0) REVERT: E 161 PHE cc_start: 0.9246 (m-80) cc_final: 0.8764 (m-80) REVERT: I 47 ASP cc_start: 0.8450 (p0) cc_final: 0.8200 (p0) REVERT: I 92 TYR cc_start: 0.8847 (t80) cc_final: 0.8521 (t80) REVERT: I 212 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8340 (t80) REVERT: F 100 MET cc_start: 0.8699 (ttp) cc_final: 0.8479 (tmm) REVERT: F 157 ILE cc_start: 0.9542 (mt) cc_final: 0.9246 (pt) REVERT: F 161 PHE cc_start: 0.9149 (m-80) cc_final: 0.8706 (m-80) REVERT: F 202 ARG cc_start: 0.9025 (mtt180) cc_final: 0.8720 (mtt180) REVERT: F 212 PHE cc_start: 0.8375 (t80) cc_final: 0.8162 (t80) REVERT: H 47 ASP cc_start: 0.8459 (p0) cc_final: 0.8209 (p0) REVERT: H 92 TYR cc_start: 0.8772 (t80) cc_final: 0.8241 (t80) REVERT: H 212 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8541 (t80) REVERT: H 230 TYR cc_start: 0.8263 (t80) cc_final: 0.7891 (t80) outliers start: 74 outliers final: 64 residues processed: 457 average time/residue: 0.1208 time to fit residues: 89.0577 Evaluate side-chains 483 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 413 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 162 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 84 optimal weight: 0.4980 chunk 180 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 99 optimal weight: 0.0010 chunk 219 optimal weight: 0.0470 chunk 201 optimal weight: 7.9990 overall best weight: 1.7088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 HIS H 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.108605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.080388 restraints weight = 43822.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.082401 restraints weight = 20889.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.083585 restraints weight = 13541.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.084210 restraints weight = 10760.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.084517 restraints weight = 9601.106| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19680 Z= 0.125 Angle : 0.667 13.216 26688 Z= 0.314 Chirality : 0.036 0.114 3024 Planarity : 0.003 0.045 3204 Dihedral : 3.919 17.477 2532 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.81 % Allowed : 22.14 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.17), residues: 2304 helix: 2.31 (0.12), residues: 1566 sheet: 0.32 (0.41), residues: 174 loop : -1.51 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 76 TYR 0.022 0.001 TYR D 230 PHE 0.018 0.001 PHE E 232 TRP 0.017 0.001 TRP B 25 HIS 0.006 0.000 HIS H 95 Details of bonding type rmsd covalent geometry : bond 0.00285 (19644) covalent geometry : angle 0.66695 (26616) SS BOND : bond 0.00135 ( 36) SS BOND : angle 0.58049 ( 72) hydrogen bonds : bond 0.04131 ( 1200) hydrogen bonds : angle 3.31675 ( 3564) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 428 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8719 (ttp) cc_final: 0.8476 (tmm) REVERT: A 155 TYR cc_start: 0.9005 (t80) cc_final: 0.8685 (t80) REVERT: A 161 PHE cc_start: 0.9133 (m-80) cc_final: 0.8636 (m-80) REVERT: G 212 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8408 (t80) REVERT: B 155 TYR cc_start: 0.8938 (t80) cc_final: 0.8583 (t80) REVERT: B 161 PHE cc_start: 0.9162 (m-80) cc_final: 0.8636 (m-80) REVERT: L 47 ASP cc_start: 0.8462 (p0) cc_final: 0.8157 (p0) REVERT: L 92 TYR cc_start: 0.8814 (t80) cc_final: 0.8558 (t80) REVERT: L 212 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8280 (t80) REVERT: C 100 MET cc_start: 0.8679 (ttp) cc_final: 0.8471 (tmm) REVERT: C 157 ILE cc_start: 0.9529 (mt) cc_final: 0.9226 (pt) REVERT: C 161 PHE cc_start: 0.9110 (m-80) cc_final: 0.8673 (m-80) REVERT: K 47 ASP cc_start: 0.8428 (p0) cc_final: 0.8170 (p0) REVERT: K 92 TYR cc_start: 0.8784 (t80) cc_final: 0.8266 (t80) REVERT: K 212 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8459 (t80) REVERT: K 230 TYR cc_start: 0.8275 (t80) cc_final: 0.7881 (t80) REVERT: D 100 MET cc_start: 0.8718 (ttp) cc_final: 0.8479 (tmm) REVERT: D 161 PHE cc_start: 0.9113 (m-80) cc_final: 0.8608 (m-80) REVERT: J 28 VAL cc_start: 0.9455 (t) cc_final: 0.9250 (m) REVERT: J 212 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8396 (t80) REVERT: E 48 GLU cc_start: 0.8540 (pt0) cc_final: 0.8339 (pt0) REVERT: E 161 PHE cc_start: 0.9217 (m-80) cc_final: 0.8713 (m-80) REVERT: I 47 ASP cc_start: 0.8374 (p0) cc_final: 0.8104 (p0) REVERT: I 92 TYR cc_start: 0.8817 (t80) cc_final: 0.8502 (t80) REVERT: I 212 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8320 (t80) REVERT: F 157 ILE cc_start: 0.9523 (mt) cc_final: 0.9230 (pt) REVERT: F 161 PHE cc_start: 0.9116 (m-80) cc_final: 0.8682 (m-80) REVERT: F 202 ARG cc_start: 0.8980 (mtt180) cc_final: 0.8698 (mtt180) REVERT: H 47 ASP cc_start: 0.8387 (p0) cc_final: 0.8137 (p0) REVERT: H 92 TYR cc_start: 0.8748 (t80) cc_final: 0.8249 (t80) REVERT: H 212 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8503 (t80) REVERT: H 230 TYR cc_start: 0.8247 (t80) cc_final: 0.7862 (t80) outliers start: 59 outliers final: 48 residues processed: 455 average time/residue: 0.1293 time to fit residues: 93.7839 Evaluate side-chains 472 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 418 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 50 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 226 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 95 HIS H 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.109185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.081104 restraints weight = 44325.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083125 restraints weight = 20709.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.084280 restraints weight = 13461.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.084891 restraints weight = 10738.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.085219 restraints weight = 9585.442| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19680 Z= 0.118 Angle : 0.659 13.983 26688 Z= 0.313 Chirality : 0.036 0.238 3024 Planarity : 0.003 0.045 3204 Dihedral : 3.810 15.156 2532 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.48 % Allowed : 22.52 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.17), residues: 2304 helix: 2.34 (0.12), residues: 1572 sheet: 0.33 (0.40), residues: 174 loop : -1.50 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 76 TYR 0.022 0.001 TYR I 230 PHE 0.029 0.001 PHE K 32 TRP 0.018 0.001 TRP C 25 HIS 0.015 0.001 HIS I 95 Details of bonding type rmsd covalent geometry : bond 0.00267 (19644) covalent geometry : angle 0.65940 (26616) SS BOND : bond 0.00109 ( 36) SS BOND : angle 0.54034 ( 72) hydrogen bonds : bond 0.03945 ( 1200) hydrogen bonds : angle 3.23322 ( 3564) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 433 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 PHE cc_start: 0.9130 (m-80) cc_final: 0.8627 (m-80) REVERT: A 223 LEU cc_start: 0.9266 (tp) cc_final: 0.9024 (tt) REVERT: G 212 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8391 (t80) REVERT: B 161 PHE cc_start: 0.9166 (m-80) cc_final: 0.8749 (m-80) REVERT: L 47 ASP cc_start: 0.8451 (p0) cc_final: 0.8132 (p0) REVERT: L 92 TYR cc_start: 0.8782 (t80) cc_final: 0.8537 (t80) REVERT: L 212 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8276 (t80) REVERT: C 157 ILE cc_start: 0.9524 (mt) cc_final: 0.9220 (pt) REVERT: C 161 PHE cc_start: 0.9103 (m-80) cc_final: 0.8673 (m-80) REVERT: K 47 ASP cc_start: 0.8415 (p0) cc_final: 0.8164 (p0) REVERT: K 92 TYR cc_start: 0.8765 (t80) cc_final: 0.8253 (t80) REVERT: K 212 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8414 (t80) REVERT: K 230 TYR cc_start: 0.8276 (t80) cc_final: 0.7888 (t80) REVERT: D 161 PHE cc_start: 0.9113 (m-80) cc_final: 0.8607 (m-80) REVERT: J 28 VAL cc_start: 0.9455 (t) cc_final: 0.9252 (m) REVERT: J 212 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8332 (t80) REVERT: E 161 PHE cc_start: 0.9223 (m-80) cc_final: 0.8729 (m-80) REVERT: I 47 ASP cc_start: 0.8372 (p0) cc_final: 0.8102 (p0) REVERT: I 92 TYR cc_start: 0.8783 (t80) cc_final: 0.8461 (t80) REVERT: I 212 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8251 (t80) REVERT: F 104 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8442 (mt-10) REVERT: F 157 ILE cc_start: 0.9526 (mt) cc_final: 0.9229 (pt) REVERT: F 161 PHE cc_start: 0.9116 (m-80) cc_final: 0.8675 (m-80) REVERT: F 202 ARG cc_start: 0.8982 (mtt180) cc_final: 0.8727 (mtt180) REVERT: H 47 ASP cc_start: 0.8380 (p0) cc_final: 0.8129 (p0) REVERT: H 92 TYR cc_start: 0.8706 (t80) cc_final: 0.8251 (t80) REVERT: H 212 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8447 (t80) REVERT: H 230 TYR cc_start: 0.8249 (t80) cc_final: 0.7872 (t80) outliers start: 52 outliers final: 44 residues processed: 459 average time/residue: 0.1249 time to fit residues: 92.6207 Evaluate side-chains 464 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 414 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 229 PHE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 212 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain K residue 229 PHE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 229 PHE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain H residue 229 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 156 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 0.1980 chunk 98 optimal weight: 10.0000 chunk 138 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 215 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.109961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.081803 restraints weight = 44287.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.083843 restraints weight = 20478.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.085056 restraints weight = 13215.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.085705 restraints weight = 10464.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.086027 restraints weight = 9333.545| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19680 Z= 0.112 Angle : 0.668 13.941 26688 Z= 0.313 Chirality : 0.036 0.232 3024 Planarity : 0.003 0.045 3204 Dihedral : 3.707 15.119 2532 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.43 % Allowed : 22.81 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.17), residues: 2304 helix: 2.43 (0.12), residues: 1572 sheet: 0.60 (0.42), residues: 162 loop : -1.66 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 76 TYR 0.022 0.001 TYR I 230 PHE 0.020 0.001 PHE E 232 TRP 0.024 0.001 TRP A 25 HIS 0.005 0.000 HIS H 95 Details of bonding type rmsd covalent geometry : bond 0.00251 (19644) covalent geometry : angle 0.66831 (26616) SS BOND : bond 0.00082 ( 36) SS BOND : angle 0.55337 ( 72) hydrogen bonds : bond 0.03702 ( 1200) hydrogen bonds : angle 3.14854 ( 3564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3575.14 seconds wall clock time: 62 minutes 35.73 seconds (3755.73 seconds total)