Starting phenix.real_space_refine on Fri Oct 30 01:24:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yg8_72915/10_2026/9yg8_72915.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yg8_72915/10_2026/9yg8_72915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yg8_72915/10_2026/9yg8_72915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yg8_72915/10_2026/9yg8_72915.map" model { file = "/net/cci-nas-00/data/ceres_data/9yg8_72915/10_2026/9yg8_72915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yg8_72915/10_2026/9yg8_72915.cif" } resolution = 3.1 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= -0.001 sd= 0.016 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 156 5.16 5 C 20925 2.51 5 N 6039 2.21 5 O 6546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33666 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1178 Classifications: {'peptide': 163} Link IDs: {'TRANS': 162} Chain: "B" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3348 Classifications: {'peptide': 463} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 440} Chain: "C" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3348 Classifications: {'peptide': 463} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 440} Chain: "D" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3348 Classifications: {'peptide': 463} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 440} Chain: "E" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1178 Classifications: {'peptide': 163} Link IDs: {'TRANS': 162} Chain: "F" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3348 Classifications: {'peptide': 463} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 440} Chain: "G" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3348 Classifications: {'peptide': 463} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 440} Chain: "H" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3348 Classifications: {'peptide': 463} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 440} Chain: "I" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1178 Classifications: {'peptide': 163} Link IDs: {'TRANS': 162} Chain: "J" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3348 Classifications: {'peptide': 463} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 440} Chain: "K" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3348 Classifications: {'peptide': 463} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 440} Chain: "L" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3348 Classifications: {'peptide': 463} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 440} Time building chain proxies: 6.72, per 1000 atoms: 0.20 Number of scatterers: 33666 At special positions: 0 Unit cell: (171.6, 162.8, 260.7, 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 156 16.00 O 6546 8.00 N 6039 7.00 C 20925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8214 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 54 sheets defined 27.8% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 921 through 952 Processing helix chain 'A' and resid 954 through 1083 removed outlier: 3.603A pdb=" N TRP A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A1044 " --> pdb=" O GLN A1040 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A1049 " --> pdb=" O ASN A1045 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A1056 " --> pdb=" O GLN A1052 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A1057 " --> pdb=" O ARG A1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.513A pdb=" N ASN B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 100 removed outlier: 3.613A pdb=" N ALA B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR B 96 " --> pdb=" O GLN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.547A pdb=" N VAL B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.781A pdb=" N GLY B 147 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 148 " --> pdb=" O ASP B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 148' Processing helix chain 'B' and resid 229 through 235 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 311 through 317 removed outlier: 3.959A pdb=" N TYR B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'C' and resid 24 through 29 Processing helix chain 'C' and resid 76 through 93 removed outlier: 3.773A pdb=" N LYS C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 99 Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.723A pdb=" N SER C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 139 Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.847A pdb=" N GLY C 147 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 148 " --> pdb=" O ASP C 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 148' Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 298 through 309 Processing helix chain 'C' and resid 312 through 317 removed outlier: 4.103A pdb=" N ARG C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.579A pdb=" N ASN D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 99 removed outlier: 3.589A pdb=" N ALA D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 108 through 116 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.710A pdb=" N VAL D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 139 Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.504A pdb=" N GLY D 147 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 235 Processing helix chain 'D' and resid 298 through 309 Processing helix chain 'E' and resid 922 through 952 Processing helix chain 'E' and resid 954 through 1083 removed outlier: 3.632A pdb=" N TRP E 966 " --> pdb=" O ALA E 962 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E1044 " --> pdb=" O GLN E1040 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA E1049 " --> pdb=" O ASN E1045 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR E1056 " --> pdb=" O GLN E1052 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E1057 " --> pdb=" O ARG E1053 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.534A pdb=" N ASN F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 100 removed outlier: 3.644A pdb=" N ALA F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP F 88 " --> pdb=" O ASP F 84 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER F 95 " --> pdb=" O ASN F 91 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N THR F 96 " --> pdb=" O GLN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 108 through 116 Processing helix chain 'F' and resid 119 through 127 removed outlier: 3.586A pdb=" N VAL F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 139 Processing helix chain 'F' and resid 144 through 148 removed outlier: 3.834A pdb=" N GLY F 147 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 148 " --> pdb=" O ASP F 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 144 through 148' Processing helix chain 'F' and resid 229 through 235 Processing helix chain 'F' and resid 298 through 309 Processing helix chain 'F' and resid 311 through 317 removed outlier: 3.986A pdb=" N TYR F 317 " --> pdb=" O GLY F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'G' and resid 24 through 29 Processing helix chain 'G' and resid 76 through 93 removed outlier: 3.780A pdb=" N LYS G 80 " --> pdb=" O GLN G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 99 Processing helix chain 'G' and resid 108 through 117 Processing helix chain 'G' and resid 119 through 128 removed outlier: 3.737A pdb=" N SER G 128 " --> pdb=" O ALA G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 139 Processing helix chain 'G' and resid 144 through 148 removed outlier: 3.801A pdb=" N GLY G 147 " --> pdb=" O GLY G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 291 Processing helix chain 'G' and resid 298 through 309 Processing helix chain 'G' and resid 312 through 317 removed outlier: 4.119A pdb=" N ARG G 316 " --> pdb=" O ALA G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 359 No H-bonds generated for 'chain 'G' and resid 357 through 359' Processing helix chain 'H' and resid 24 through 29 removed outlier: 3.590A pdb=" N ASN H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 99 removed outlier: 3.566A pdb=" N ALA H 83 " --> pdb=" O SER H 79 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 89 " --> pdb=" O GLN H 85 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA H 99 " --> pdb=" O SER H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 116 Processing helix chain 'H' and resid 119 through 127 removed outlier: 3.687A pdb=" N VAL H 127 " --> pdb=" O LYS H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 139 Processing helix chain 'H' and resid 144 through 148 Processing helix chain 'H' and resid 229 through 235 Processing helix chain 'H' and resid 298 through 309 Processing helix chain 'I' and resid 922 through 952 Processing helix chain 'I' and resid 954 through 1083 removed outlier: 3.602A pdb=" N TRP I 966 " --> pdb=" O ALA I 962 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA I1044 " --> pdb=" O GLN I1040 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA I1049 " --> pdb=" O ASN I1045 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR I1056 " --> pdb=" O GLN I1052 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL I1057 " --> pdb=" O ARG I1053 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 removed outlier: 3.522A pdb=" N ASN J 28 " --> pdb=" O ALA J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 84 removed outlier: 3.613A pdb=" N ALA J 81 " --> pdb=" O GLY J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 100 removed outlier: 3.569A pdb=" N GLN J 92 " --> pdb=" O ASP J 88 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER J 95 " --> pdb=" O ASN J 91 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N THR J 96 " --> pdb=" O GLN J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 105 Processing helix chain 'J' and resid 108 through 116 Processing helix chain 'J' and resid 119 through 127 removed outlier: 3.592A pdb=" N VAL J 127 " --> pdb=" O LYS J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 139 Processing helix chain 'J' and resid 144 through 148 removed outlier: 3.868A pdb=" N GLY J 147 " --> pdb=" O GLY J 144 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE J 148 " --> pdb=" O ASP J 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 144 through 148' Processing helix chain 'J' and resid 229 through 235 Processing helix chain 'J' and resid 298 through 309 Processing helix chain 'J' and resid 311 through 317 removed outlier: 3.977A pdb=" N TYR J 317 " --> pdb=" O GLY J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 357 through 359 No H-bonds generated for 'chain 'J' and resid 357 through 359' Processing helix chain 'K' and resid 24 through 29 Processing helix chain 'K' and resid 76 through 93 removed outlier: 3.810A pdb=" N LYS K 80 " --> pdb=" O GLN K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 99 Processing helix chain 'K' and resid 108 through 117 Processing helix chain 'K' and resid 119 through 128 removed outlier: 3.734A pdb=" N SER K 128 " --> pdb=" O ALA K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 139 Processing helix chain 'K' and resid 144 through 148 removed outlier: 3.814A pdb=" N GLY K 147 " --> pdb=" O GLY K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 291 Processing helix chain 'K' and resid 298 through 309 Processing helix chain 'K' and resid 312 through 317 removed outlier: 4.094A pdb=" N ARG K 316 " --> pdb=" O ALA K 312 " (cutoff:3.500A) Processing helix chain 'K' and resid 357 through 359 No H-bonds generated for 'chain 'K' and resid 357 through 359' Processing helix chain 'L' and resid 24 through 29 removed outlier: 3.590A pdb=" N ASN L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 99 removed outlier: 3.587A pdb=" N ALA L 83 " --> pdb=" O SER L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 116 Processing helix chain 'L' and resid 119 through 127 removed outlier: 3.709A pdb=" N VAL L 127 " --> pdb=" O LYS L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 139 Processing helix chain 'L' and resid 144 through 148 Processing helix chain 'L' and resid 229 through 235 removed outlier: 3.500A pdb=" N ALA L 233 " --> pdb=" O THR L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 309 Processing sheet with id=AA1, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.599A pdb=" N GLY B 67 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL B 9 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 8 " --> pdb=" O SER B 21 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B 55 " --> pdb=" O GLY B 46 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 71 " --> pdb=" O ARG B 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 168 through 172 removed outlier: 3.538A pdb=" N GLY B 168 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 198 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 168 through 172 removed outlier: 3.538A pdb=" N GLY B 168 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 198 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 270 through 271 Processing sheet with id=AA5, first strand: chain 'B' and resid 276 through 279 removed outlier: 3.571A pdb=" N MET B 278 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 433 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL B 365 " --> pdb=" O PRO B 439 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP B 441 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR B 363 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 413 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 387 " --> pdb=" O LYS B 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AA7, first strand: chain 'C' and resid 65 through 68 removed outlier: 5.182A pdb=" N ASN C 66 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 11 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 8 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL C 53 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL C 48 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR C 55 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 168 through 172 removed outlier: 3.543A pdb=" N GLY C 198 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 168 through 172 removed outlier: 3.543A pdb=" N GLY C 198 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 270 through 271 Processing sheet with id=AB2, first strand: chain 'C' and resid 276 through 282 removed outlier: 6.305A pdb=" N VAL C 323 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N HIS C 322 " --> pdb=" O CYS C 438 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N CYS C 438 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 434 " --> pdb=" O MET C 326 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA C 433 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL C 365 " --> pdb=" O PRO C 439 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TRP C 441 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR C 363 " --> pdb=" O TRP C 441 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C 362 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 413 " --> pdb=" O ALA C 362 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL C 387 " --> pdb=" O LYS C 394 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 335 through 337 removed outlier: 3.521A pdb=" N MET C 375 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 65 through 68 removed outlier: 5.258A pdb=" N ASN D 66 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL D 11 " --> pdb=" O ASN D 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 19 " --> pdb=" O SER D 10 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL D 53 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL D 48 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR D 55 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 168 through 172 removed outlier: 3.647A pdb=" N TYR D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY D 198 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 168 through 172 removed outlier: 3.647A pdb=" N TYR D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY D 198 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N MET D 211 " --> pdb=" O ILE D 227 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 270 through 271 Processing sheet with id=AB8, first strand: chain 'D' and resid 270 through 271 removed outlier: 7.839A pdb=" N PHE D 426 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS D 398 " --> pdb=" O ILE D 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 276 through 282 removed outlier: 5.779A pdb=" N VAL D 323 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N HIS D 322 " --> pdb=" O CYS D 438 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N CYS D 438 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL D 365 " --> pdb=" O PRO D 439 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP D 441 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR D 363 " --> pdb=" O TRP D 441 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR D 413 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL D 387 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 65 through 68 removed outlier: 3.662A pdb=" N GLY F 67 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL F 9 " --> pdb=" O GLY F 67 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR F 8 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER F 71 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 168 through 172 removed outlier: 3.515A pdb=" N GLY F 168 " --> pdb=" O HIS F 190 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY F 198 " --> pdb=" O LYS F 216 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 168 through 172 removed outlier: 3.515A pdb=" N GLY F 168 " --> pdb=" O HIS F 190 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY F 198 " --> pdb=" O LYS F 216 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 270 through 271 Processing sheet with id=AC5, first strand: chain 'F' and resid 276 through 279 removed outlier: 6.401A pdb=" N ALA F 433 " --> pdb=" O GLU F 371 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL F 365 " --> pdb=" O PRO F 439 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP F 441 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR F 363 " --> pdb=" O TRP F 441 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR F 413 " --> pdb=" O ALA F 362 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL F 387 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 335 through 337 removed outlier: 3.682A pdb=" N PHE F 345 " --> pdb=" O THR F 428 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 65 through 68 removed outlier: 5.160A pdb=" N ASN G 66 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL G 11 " --> pdb=" O ASN G 66 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR G 8 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL G 53 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL G 48 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR G 55 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 168 through 172 removed outlier: 3.573A pdb=" N GLY G 198 " --> pdb=" O LYS G 216 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 168 through 172 removed outlier: 3.573A pdb=" N GLY G 198 " --> pdb=" O LYS G 216 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 270 through 271 Processing sheet with id=AD2, first strand: chain 'G' and resid 276 through 282 removed outlier: 6.226A pdb=" N VAL G 323 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N HIS G 322 " --> pdb=" O CYS G 438 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N CYS G 438 " --> pdb=" O HIS G 322 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA G 433 " --> pdb=" O GLU G 371 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL G 365 " --> pdb=" O PRO G 439 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TRP G 441 " --> pdb=" O THR G 363 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR G 363 " --> pdb=" O TRP G 441 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA G 362 " --> pdb=" O THR G 413 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR G 413 " --> pdb=" O ALA G 362 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL G 387 " --> pdb=" O LYS G 394 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 335 through 337 removed outlier: 3.526A pdb=" N MET G 375 " --> pdb=" O LEU G 400 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 65 through 68 removed outlier: 5.284A pdb=" N ASN H 66 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL H 11 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR H 19 " --> pdb=" O SER H 10 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL H 53 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL H 48 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR H 55 " --> pdb=" O GLY H 46 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 168 through 172 removed outlier: 3.657A pdb=" N TYR H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY H 198 " --> pdb=" O LYS H 216 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 168 through 172 removed outlier: 3.657A pdb=" N TYR H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY H 198 " --> pdb=" O LYS H 216 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N MET H 211 " --> pdb=" O ILE H 227 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 270 through 271 Processing sheet with id=AD8, first strand: chain 'H' and resid 270 through 271 removed outlier: 7.839A pdb=" N PHE H 426 " --> pdb=" O ALA H 347 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS H 398 " --> pdb=" O ILE H 377 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 276 through 282 removed outlier: 5.809A pdb=" N VAL H 323 " --> pdb=" O GLY H 280 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N HIS H 322 " --> pdb=" O CYS H 438 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N CYS H 438 " --> pdb=" O HIS H 322 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA H 433 " --> pdb=" O GLU H 371 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL H 365 " --> pdb=" O PRO H 439 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TRP H 441 " --> pdb=" O THR H 363 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR H 363 " --> pdb=" O TRP H 441 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR H 413 " --> pdb=" O ALA H 362 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL H 387 " --> pdb=" O LYS H 394 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 65 through 68 removed outlier: 3.603A pdb=" N GLY J 67 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL J 9 " --> pdb=" O GLY J 67 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR J 8 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR J 55 " --> pdb=" O GLY J 46 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER J 71 " --> pdb=" O ARG J 36 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 168 through 172 removed outlier: 3.508A pdb=" N GLY J 168 " --> pdb=" O HIS J 190 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR J 197 " --> pdb=" O GLN J 193 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY J 198 " --> pdb=" O LYS J 216 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 168 through 172 removed outlier: 3.508A pdb=" N GLY J 168 " --> pdb=" O HIS J 190 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR J 197 " --> pdb=" O GLN J 193 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY J 198 " --> pdb=" O LYS J 216 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 270 through 271 Processing sheet with id=AE5, first strand: chain 'J' and resid 276 through 279 removed outlier: 3.578A pdb=" N MET J 278 " --> pdb=" O VAL J 325 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA J 433 " --> pdb=" O GLU J 371 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL J 365 " --> pdb=" O PRO J 439 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TRP J 441 " --> pdb=" O THR J 363 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR J 363 " --> pdb=" O TRP J 441 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR J 413 " --> pdb=" O ALA J 362 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL J 387 " --> pdb=" O LYS J 394 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 335 through 337 removed outlier: 3.551A pdb=" N PHE J 345 " --> pdb=" O THR J 428 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 65 through 68 removed outlier: 5.204A pdb=" N ASN K 66 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL K 11 " --> pdb=" O ASN K 66 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR K 8 " --> pdb=" O SER K 21 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL K 53 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL K 48 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR K 55 " --> pdb=" O GLY K 46 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 168 through 172 removed outlier: 3.533A pdb=" N GLY K 198 " --> pdb=" O LYS K 216 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 168 through 172 removed outlier: 3.533A pdb=" N GLY K 198 " --> pdb=" O LYS K 216 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 270 through 271 Processing sheet with id=AF2, first strand: chain 'K' and resid 276 through 282 removed outlier: 6.293A pdb=" N VAL K 323 " --> pdb=" O GLY K 280 " (cutoff:3.500A) removed outlier: 10.112A pdb=" N HIS K 322 " --> pdb=" O CYS K 438 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N CYS K 438 " --> pdb=" O HIS K 322 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL K 434 " --> pdb=" O MET K 326 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL K 365 " --> pdb=" O PRO K 439 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TRP K 441 " --> pdb=" O THR K 363 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR K 363 " --> pdb=" O TRP K 441 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA K 362 " --> pdb=" O THR K 413 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR K 413 " --> pdb=" O ALA K 362 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL K 387 " --> pdb=" O LYS K 394 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 335 through 337 removed outlier: 3.505A pdb=" N MET K 375 " --> pdb=" O LEU K 400 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 65 through 68 removed outlier: 5.247A pdb=" N ASN L 66 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL L 11 " --> pdb=" O ASN L 66 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR L 19 " --> pdb=" O SER L 10 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL L 53 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL L 48 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR L 55 " --> pdb=" O GLY L 46 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 168 through 172 removed outlier: 3.642A pdb=" N TYR L 197 " --> pdb=" O GLN L 193 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY L 198 " --> pdb=" O LYS L 216 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 168 through 172 removed outlier: 3.642A pdb=" N TYR L 197 " --> pdb=" O GLN L 193 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY L 198 " --> pdb=" O LYS L 216 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N MET L 211 " --> pdb=" O ILE L 227 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 270 through 271 Processing sheet with id=AF8, first strand: chain 'L' and resid 270 through 271 removed outlier: 7.855A pdb=" N PHE L 426 " --> pdb=" O ALA L 347 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS L 398 " --> pdb=" O ILE L 377 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 276 through 282 removed outlier: 5.797A pdb=" N VAL L 323 " --> pdb=" O GLY L 280 " (cutoff:3.500A) removed outlier: 10.035A pdb=" N HIS L 322 " --> pdb=" O CYS L 438 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N CYS L 438 " --> pdb=" O HIS L 322 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL L 365 " --> pdb=" O PRO L 439 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TRP L 441 " --> pdb=" O THR L 363 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR L 363 " --> pdb=" O TRP L 441 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR L 413 " --> pdb=" O ALA L 362 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL L 387 " --> pdb=" O LYS L 394 " (cutoff:3.500A) 1679 hydrogen bonds defined for protein. 4587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.31 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8628 1.33 - 1.45: 6932 1.45 - 1.57: 18547 1.57 - 1.69: 0 1.69 - 1.81: 294 Bond restraints: 34401 Sorted by residual: bond pdb=" CA SER C 50 " pdb=" CB SER C 50 " ideal model delta sigma weight residual 1.539 1.492 0.047 1.36e-02 5.41e+03 1.18e+01 bond pdb=" N TYR J 317 " pdb=" CA TYR J 317 " ideal model delta sigma weight residual 1.452 1.486 -0.034 1.22e-02 6.72e+03 7.59e+00 bond pdb=" N LEU F 304 " pdb=" CA LEU F 304 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.20e-02 6.94e+03 7.14e+00 bond pdb=" N TYR F 317 " pdb=" CA TYR F 317 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.16e-02 7.43e+03 6.95e+00 bond pdb=" N TYR B 317 " pdb=" CA TYR B 317 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.16e-02 7.43e+03 6.76e+00 ... (remaining 34396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 45688 1.31 - 2.61: 1064 2.61 - 3.92: 217 3.92 - 5.22: 20 5.22 - 6.53: 9 Bond angle restraints: 46998 Sorted by residual: angle pdb=" C GLN F 306 " pdb=" N THR F 307 " pdb=" CA THR F 307 " ideal model delta sigma weight residual 121.54 115.81 5.73 1.91e+00 2.74e-01 9.01e+00 angle pdb=" CA TRP F 263 " pdb=" C TRP F 263 " pdb=" O TRP F 263 " ideal model delta sigma weight residual 121.56 118.29 3.27 1.09e+00 8.42e-01 8.99e+00 angle pdb=" CA GLN F 194 " pdb=" CB GLN F 194 " pdb=" CG GLN F 194 " ideal model delta sigma weight residual 114.10 119.89 -5.79 2.00e+00 2.50e-01 8.37e+00 angle pdb=" CA GLY B 318 " pdb=" C GLY B 318 " pdb=" O GLY B 318 " ideal model delta sigma weight residual 121.05 118.48 2.57 9.00e-01 1.23e+00 8.18e+00 angle pdb=" CA ILE I1068 " pdb=" C ILE I1068 " pdb=" O ILE I1068 " ideal model delta sigma weight residual 121.17 118.21 2.96 1.06e+00 8.90e-01 7.80e+00 ... (remaining 46993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 17513 17.35 - 34.71: 1855 34.71 - 52.06: 429 52.06 - 69.42: 75 69.42 - 86.77: 27 Dihedral angle restraints: 19899 sinusoidal: 6924 harmonic: 12975 Sorted by residual: dihedral pdb=" CA ASP J 160 " pdb=" CB ASP J 160 " pdb=" CG ASP J 160 " pdb=" OD1 ASP J 160 " ideal model delta sinusoidal sigma weight residual -30.00 -88.52 58.52 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP B 160 " pdb=" CB ASP B 160 " pdb=" CG ASP B 160 " pdb=" OD1 ASP B 160 " ideal model delta sinusoidal sigma weight residual -30.00 -87.45 57.45 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CG ARG L 87 " pdb=" CD ARG L 87 " pdb=" NE ARG L 87 " pdb=" CZ ARG L 87 " ideal model delta sinusoidal sigma weight residual 90.00 134.47 -44.47 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 19896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3928 0.040 - 0.081: 870 0.081 - 0.121: 478 0.121 - 0.162: 38 0.162 - 0.202: 2 Chirality restraints: 5316 Sorted by residual: chirality pdb=" CA ILE I1068 " pdb=" N ILE I1068 " pdb=" C ILE I1068 " pdb=" CB ILE I1068 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU F 305 " pdb=" N LEU F 305 " pdb=" C LEU F 305 " pdb=" CB LEU F 305 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA ILE G 165 " pdb=" N ILE G 165 " pdb=" C ILE G 165 " pdb=" CB ILE G 165 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 5313 not shown) Planarity restraints: 6189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I1015 " 0.269 9.50e-02 1.11e+02 1.21e-01 8.97e+00 pdb=" NE ARG I1015 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG I1015 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG I1015 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG I1015 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 109 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO F 110 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO F 110 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 110 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1015 " -0.196 9.50e-02 1.11e+02 8.79e-02 4.75e+00 pdb=" NE ARG A1015 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A1015 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A1015 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A1015 " -0.008 2.00e-02 2.50e+03 ... (remaining 6186 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1608 2.73 - 3.27: 32170 3.27 - 3.81: 54527 3.81 - 4.36: 65029 4.36 - 4.90: 119668 Nonbonded interactions: 273002 Sorted by model distance: nonbonded pdb=" OG SER K 10 " pdb=" OD1 ASN K 66 " model vdw 2.182 3.040 nonbonded pdb=" OG1 THR B 363 " pdb=" O GLY B 444 " model vdw 2.207 3.040 nonbonded pdb=" OG SER G 10 " pdb=" OD1 ASN G 66 " model vdw 2.209 3.040 nonbonded pdb=" O SER L 154 " pdb=" OG SER L 154 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR J 363 " pdb=" O GLY J 444 " model vdw 2.214 3.040 ... (remaining 272997 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 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.120 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34401 Z= 0.161 Angle : 0.509 6.527 46998 Z= 0.291 Chirality : 0.043 0.202 5316 Planarity : 0.005 0.121 6189 Dihedral : 15.109 86.774 11685 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.21 % Allowed : 20.93 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.87 (0.12), residues: 4632 helix: 2.89 (0.15), residues: 1098 sheet: 0.17 (0.16), residues: 981 loop : -0.27 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1021 TYR 0.010 0.001 TYR K 78 PHE 0.011 0.001 PHE F 35 TRP 0.021 0.001 TRP J 221 HIS 0.006 0.001 HIS F 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (34401) covalent geometry : angle 0.50880 / 0.29 (46998) hydrogen bonds : bond 0.20213 / 13.92 ( 1517) hydrogen bonds : angle 7.08115 / 5.05 ( 4587) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 342 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 MET cc_start: 0.8216 (ttp) cc_final: 0.7960 (ttt) REVERT: B 404 GLU cc_start: 0.8778 (mp0) cc_final: 0.8131 (mp0) REVERT: B 416 TRP cc_start: 0.8121 (OUTLIER) cc_final: 0.7106 (p-90) REVERT: D 404 GLU cc_start: 0.8664 (mp0) cc_final: 0.8098 (mp0) REVERT: E 1039 GLU cc_start: 0.8992 (tp30) cc_final: 0.8572 (tp30) REVERT: F 404 GLU cc_start: 0.8818 (mp0) cc_final: 0.8253 (mp0) REVERT: F 416 TRP cc_start: 0.8176 (OUTLIER) cc_final: 0.6922 (p-90) REVERT: H 374 SER cc_start: 0.9439 (OUTLIER) cc_final: 0.9123 (p) REVERT: I 1039 GLU cc_start: 0.8830 (tp30) cc_final: 0.8548 (tp30) REVERT: J 326 MET cc_start: 0.8425 (ttp) cc_final: 0.8158 (ttt) REVERT: J 404 GLU cc_start: 0.8714 (mp0) cc_final: 0.8248 (mp0) REVERT: J 416 TRP cc_start: 0.8010 (OUTLIER) cc_final: 0.7282 (p-90) REVERT: L 401 THR cc_start: 0.8784 (p) cc_final: 0.8012 (t) REVERT: L 404 GLU cc_start: 0.8756 (mp0) cc_final: 0.8378 (mp0) outliers start: 7 outliers final: 0 residues processed: 346 average time/residue: 0.2035 time to fit residues: 116.1886 Evaluate side-chains 270 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 266 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain J residue 416 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: [432, 197, 388, 455, 215, 20, 132, 261, 248, 207, 401] chunk 432 optimal weight: 0.0010 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 8.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 68 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN ** D 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN F 261 GLN ** G 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 222 GLN ** H 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 222 GLN ** L 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.062310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.043357 restraints weight = 105448.157| |-----------------------------------------------------------------------------| r_work (start): 0.2574 rms_B_bonded: 3.38 r_work: 0.2441 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 34401 Z= 0.401 Angle : 0.686 7.974 46998 Z= 0.370 Chirality : 0.049 0.196 5316 Planarity : 0.005 0.058 6189 Dihedral : 4.565 41.757 4969 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.85 % Allowed : 20.36 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.57 (0.12), residues: 4632 helix: 2.73 (0.15), residues: 1116 sheet: 0.11 (0.16), residues: 975 loop : -0.58 (0.11), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 247 TYR 0.019 0.002 TYR K 78 PHE 0.021 0.002 PHE H 423 TRP 0.015 0.002 TRP K 263 HIS 0.009 0.002 HIS C 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00945 / 0.40 (34401) covalent geometry : angle 0.68644 / 0.37 (46998) hydrogen bonds : bond 0.07587 / 5.30 ( 1517) hydrogen bonds : angle 5.22926 / 3.76 ( 4587) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 258 time to evaluate : 1.201 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 1064 ASN cc_start: 0.6880 (t0) cc_final: 0.6652 (t0) REVERT: B 278 MET cc_start: 0.8026 (pmm) cc_final: 0.7781 (pmm) REVERT: B 296 GLU cc_start: 0.9097 (tp30) cc_final: 0.8811 (mm-30) REVERT: B 366 MET cc_start: 0.8344 (ptt) cc_final: 0.8139 (ptt) REVERT: B 404 GLU cc_start: 0.8977 (mp0) cc_final: 0.8483 (mp0) REVERT: B 416 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.7172 (p-90) REVERT: C 320 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8465 (mt-10) REVERT: C 360 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8144 (mp10) REVERT: D 401 THR cc_start: 0.8991 (p) cc_final: 0.8264 (p) REVERT: D 404 GLU cc_start: 0.8732 (mp0) cc_final: 0.7881 (mp0) REVERT: E 975 GLU cc_start: 0.8958 (tp30) cc_final: 0.8664 (tp30) REVERT: F 242 MET cc_start: 0.7963 (mtm) cc_final: 0.7715 (mtp) REVERT: F 296 GLU cc_start: 0.9186 (tp30) cc_final: 0.8977 (mm-30) REVERT: F 404 GLU cc_start: 0.8829 (mp0) cc_final: 0.8374 (mp0) REVERT: G 42 TRP cc_start: 0.9415 (OUTLIER) cc_final: 0.9099 (m-10) REVERT: G 320 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8644 (mt-10) REVERT: G 353 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8295 (mmp80) REVERT: H 335 GLU cc_start: 0.8784 (tp30) cc_final: 0.8522 (tp30) REVERT: I 931 ASP cc_start: 0.9014 (t70) cc_final: 0.8773 (m-30) REVERT: I 1039 GLU cc_start: 0.8858 (tp30) cc_final: 0.8628 (tp30) REVERT: J 216 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7213 (pttp) REVERT: J 278 MET cc_start: 0.8046 (pmm) cc_final: 0.7802 (pmm) REVERT: J 404 GLU cc_start: 0.8826 (mp0) cc_final: 0.8364 (mp0) REVERT: J 416 TRP cc_start: 0.8498 (OUTLIER) cc_final: 0.7242 (p-90) REVERT: K 42 TRP cc_start: 0.9358 (OUTLIER) cc_final: 0.9013 (m-10) outliers start: 129 outliers final: 75 residues processed: 375 average time/residue: 0.1762 time to fit residues: 114.7114 Evaluate side-chains 331 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 249 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain E residue 993 LEU Chi-restraints excluded: chain E residue 1056 THR Chi-restraints excluded: chain E residue 1061 THR Chi-restraints excluded: chain E residue 1070 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 353 ARG Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 257 ILE Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain I residue 1056 THR Chi-restraints excluded: chain I residue 1061 THR Chi-restraints excluded: chain J residue 143 VAL Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 379 THR Chi-restraints excluded: chain J residue 395 SER Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 416 TRP Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 42 TRP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain K residue 355 LEU Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 434 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 257 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: [290, 397, 35, 185, 64, 84, 126, 414, 136, 451, 275] chunk 290 optimal weight: 0.9980 chunk 397 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 414 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 451 optimal weight: 0.9990 chunk 275 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 HIS C 360 GLN D 200 GLN ** D 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 322 HIS H 200 GLN ** H 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 322 HIS ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 GLN ** L 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.046615 restraints weight = 102206.117| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 3.39 r_work: 0.2524 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34401 Z= 0.126 Angle : 0.486 5.935 46998 Z= 0.264 Chirality : 0.043 0.173 5316 Planarity : 0.004 0.052 6189 Dihedral : 4.100 39.737 4968 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.39 % Allowed : 22.12 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 1.03 (0.12), residues: 4632 helix: 3.29 (0.15), residues: 1116 sheet: 0.36 (0.17), residues: 912 loop : -0.37 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 214 TYR 0.008 0.001 TYR H 425 PHE 0.014 0.001 PHE L 423 TRP 0.013 0.001 TRP H 103 HIS 0.007 0.001 HIS F 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (34401) covalent geometry : angle 0.48606 / 0.26 (46998) hydrogen bonds : bond 0.06279 / 4.40 ( 1517) hydrogen bonds : angle 4.59566 / 3.28 ( 4587) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 270 time to evaluate : 1.021 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: B 272 TRP cc_start: 0.7761 (OUTLIER) cc_final: 0.6342 (t60) REVERT: B 346 LEU cc_start: 0.9209 (tt) cc_final: 0.8523 (tt) REVERT: B 366 MET cc_start: 0.8383 (ptt) cc_final: 0.8117 (ptt) REVERT: B 404 GLU cc_start: 0.8933 (mp0) cc_final: 0.8579 (mp0) REVERT: B 416 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7149 (p-90) REVERT: C 320 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8393 (mt-10) REVERT: C 360 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8082 (mp10) REVERT: D 375 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8812 (ttp) REVERT: D 404 GLU cc_start: 0.8728 (mp0) cc_final: 0.7941 (mp0) REVERT: E 929 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8862 (pp20) REVERT: E 984 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8479 (mt-10) REVERT: F 272 TRP cc_start: 0.7698 (OUTLIER) cc_final: 0.6800 (t60) REVERT: F 296 GLU cc_start: 0.9114 (tp30) cc_final: 0.8829 (mm-30) REVERT: F 404 GLU cc_start: 0.8770 (mp0) cc_final: 0.8283 (mp0) REVERT: F 416 TRP cc_start: 0.8091 (OUTLIER) cc_final: 0.6754 (p-90) REVERT: G 306 GLN cc_start: 0.9590 (tt0) cc_final: 0.9322 (pt0) REVERT: G 320 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8577 (mt-10) REVERT: G 404 GLU cc_start: 0.8881 (mp0) cc_final: 0.8639 (mp0) REVERT: H 335 GLU cc_start: 0.8747 (tp30) cc_final: 0.8470 (tp30) REVERT: J 150 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8045 (tt) REVERT: J 216 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7183 (pttp) REVERT: J 278 MET cc_start: 0.8034 (pmm) cc_final: 0.7827 (pmm) REVERT: J 296 GLU cc_start: 0.9221 (tp30) cc_final: 0.8859 (mm-30) REVERT: J 357 CYS cc_start: 0.8789 (m) cc_final: 0.8476 (p) REVERT: J 404 GLU cc_start: 0.8800 (mp0) cc_final: 0.8334 (mp0) REVERT: J 416 TRP cc_start: 0.8283 (OUTLIER) cc_final: 0.7215 (p-90) REVERT: K 326 MET cc_start: 0.9145 (ttp) cc_final: 0.8901 (ttp) outliers start: 80 outliers final: 39 residues processed: 327 average time/residue: 0.1845 time to fit residues: 104.2355 Evaluate side-chains 305 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain I residue 929 GLU Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain I residue 993 LEU Chi-restraints excluded: chain I residue 1070 THR Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 379 THR Chi-restraints excluded: chain J residue 416 TRP Chi-restraints excluded: chain K residue 355 LEU Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 429 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: [414, 432, 156, 333, 423, 199, 76, 427, 284, 183, 391] chunk 414 optimal weight: 4.9990 chunk 432 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 333 optimal weight: 0.9980 chunk 423 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 427 optimal weight: 0.7980 chunk 284 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 391 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN ** D 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.064219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.045328 restraints weight = 102924.321| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 3.39 r_work: 0.2498 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34401 Z= 0.183 Angle : 0.508 9.275 46998 Z= 0.272 Chirality : 0.043 0.171 5316 Planarity : 0.004 0.053 6189 Dihedral : 4.076 39.425 4968 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.77 % Allowed : 22.21 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 1.07 (0.12), residues: 4632 helix: 3.37 (0.15), residues: 1116 sheet: 0.38 (0.17), residues: 912 loop : -0.35 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 369 TYR 0.010 0.001 TYR C 60 PHE 0.015 0.001 PHE L 423 TRP 0.021 0.001 TRP G 416 HIS 0.007 0.001 HIS F 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (34401) covalent geometry : angle 0.50777 / 0.27 (46998) hydrogen bonds : bond 0.06347 / 4.45 ( 1517) hydrogen bonds : angle 4.52227 / 3.23 ( 4587) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 261 time to evaluate : 1.226 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: B 272 TRP cc_start: 0.7803 (OUTLIER) cc_final: 0.6342 (t60) REVERT: B 320 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: B 346 LEU cc_start: 0.9249 (tt) cc_final: 0.8560 (tt) REVERT: B 404 GLU cc_start: 0.8959 (mp0) cc_final: 0.8498 (mp0) REVERT: B 416 TRP cc_start: 0.8373 (OUTLIER) cc_final: 0.7253 (p-90) REVERT: C 320 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8322 (mt-10) REVERT: C 360 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7995 (mp10) REVERT: D 404 GLU cc_start: 0.8759 (mp0) cc_final: 0.7998 (mp0) REVERT: E 984 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8472 (mt-10) REVERT: F 272 TRP cc_start: 0.7731 (OUTLIER) cc_final: 0.6758 (t60) REVERT: F 296 GLU cc_start: 0.9105 (tp30) cc_final: 0.8805 (mm-30) REVERT: F 404 GLU cc_start: 0.8771 (mp0) cc_final: 0.8290 (mp0) REVERT: F 416 TRP cc_start: 0.8131 (OUTLIER) cc_final: 0.6801 (p-90) REVERT: G 42 TRP cc_start: 0.9356 (OUTLIER) cc_final: 0.9034 (m-10) REVERT: G 320 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8680 (mt-10) REVERT: G 353 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8225 (mmp80) REVERT: H 335 GLU cc_start: 0.8818 (tp30) cc_final: 0.8535 (tp30) REVERT: I 999 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8890 (t70) REVERT: J 216 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7253 (pttp) REVERT: J 296 GLU cc_start: 0.9209 (tp30) cc_final: 0.8777 (mm-30) REVERT: J 357 CYS cc_start: 0.8684 (m) cc_final: 0.8425 (p) REVERT: J 404 GLU cc_start: 0.8786 (mp0) cc_final: 0.8319 (mp0) REVERT: J 416 TRP cc_start: 0.8335 (OUTLIER) cc_final: 0.7210 (p-90) REVERT: K 320 GLU cc_start: 0.8694 (mt-10) cc_final: 0.7898 (pt0) REVERT: L 214 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7343 (ptt180) outliers start: 93 outliers final: 58 residues processed: 338 average time/residue: 0.1811 time to fit residues: 105.5250 Evaluate side-chains 325 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 255 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 999 ASP Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 353 ARG Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 401 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 257 ILE Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain I residue 993 LEU Chi-restraints excluded: chain I residue 999 ASP Chi-restraints excluded: chain I residue 1070 THR Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 272 TRP Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 379 THR Chi-restraints excluded: chain J residue 416 TRP Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain K residue 355 LEU Chi-restraints excluded: chain K residue 360 GLN Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 434 VAL Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 214 ARG Chi-restraints excluded: chain L residue 257 ILE Chi-restraints excluded: chain L residue 330 ILE Chi-restraints excluded: chain L residue 429 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: [149, 153, 262, 157, 361, 85, 427, 242, 202, 409, 53] chunk 149 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 262 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 361 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 427 optimal weight: 4.9990 chunk 242 optimal weight: 0.0030 chunk 202 optimal weight: 0.6980 chunk 409 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN ** D 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.065108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.046284 restraints weight = 103072.880| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 3.39 r_work: 0.2524 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34401 Z= 0.132 Angle : 0.474 8.681 46998 Z= 0.255 Chirality : 0.043 0.166 5316 Planarity : 0.004 0.051 6189 Dihedral : 3.951 39.372 4968 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.80 % Allowed : 22.42 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 1.20 (0.12), residues: 4632 helix: 3.53 (0.15), residues: 1116 sheet: 0.41 (0.17), residues: 912 loop : -0.28 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 214 TYR 0.008 0.001 TYR C 60 PHE 0.013 0.001 PHE L 423 TRP 0.011 0.001 TRP D 103 HIS 0.007 0.001 HIS H 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (34401) covalent geometry : angle 0.47401 / 0.25 (46998) hydrogen bonds : bond 0.06019 / 4.22 ( 1517) hydrogen bonds : angle 4.33403 / 3.09 ( 4587) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 265 time to evaluate : 1.249 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: B 272 TRP cc_start: 0.7900 (OUTLIER) cc_final: 0.6434 (t60) REVERT: B 320 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7152 (pm20) REVERT: B 346 LEU cc_start: 0.9247 (tt) cc_final: 0.8578 (tt) REVERT: B 404 GLU cc_start: 0.8936 (mp0) cc_final: 0.8546 (mp0) REVERT: B 416 TRP cc_start: 0.8333 (OUTLIER) cc_final: 0.7329 (p-90) REVERT: C 320 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8342 (mt-10) REVERT: C 360 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: C 400 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9069 (mp) REVERT: D 278 MET cc_start: 0.8873 (mmm) cc_final: 0.8634 (mtm) REVERT: D 404 GLU cc_start: 0.8812 (mp0) cc_final: 0.8087 (mp0) REVERT: F 216 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7593 (ptmm) REVERT: F 272 TRP cc_start: 0.7796 (OUTLIER) cc_final: 0.6564 (t60) REVERT: F 296 GLU cc_start: 0.9126 (tp30) cc_final: 0.8848 (mm-30) REVERT: F 346 LEU cc_start: 0.9257 (tt) cc_final: 0.8726 (tt) REVERT: F 404 GLU cc_start: 0.8775 (mp0) cc_final: 0.8310 (mp0) REVERT: F 416 TRP cc_start: 0.8057 (OUTLIER) cc_final: 0.6773 (p-90) REVERT: G 42 TRP cc_start: 0.9352 (OUTLIER) cc_final: 0.9045 (m-10) REVERT: G 320 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8694 (mt-10) REVERT: H 278 MET cc_start: 0.8914 (mmm) cc_final: 0.8642 (mmm) REVERT: H 335 GLU cc_start: 0.8817 (tp30) cc_final: 0.8525 (tp30) REVERT: I 999 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8887 (t70) REVERT: J 150 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8075 (tt) REVERT: J 216 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7313 (pttp) REVERT: J 278 MET cc_start: 0.7880 (pmm) cc_final: 0.7661 (pmm) REVERT: J 404 GLU cc_start: 0.8795 (mp0) cc_final: 0.8334 (mp0) REVERT: J 416 TRP cc_start: 0.8161 (OUTLIER) cc_final: 0.7021 (p-90) REVERT: K 320 GLU cc_start: 0.8721 (mt-10) cc_final: 0.7865 (pt0) outliers start: 94 outliers final: 60 residues processed: 340 average time/residue: 0.1825 time to fit residues: 107.3741 Evaluate side-chains 330 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 257 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 1061 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain I residue 993 LEU Chi-restraints excluded: chain I residue 999 ASP Chi-restraints excluded: chain I residue 1056 THR Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 272 TRP Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 379 THR Chi-restraints excluded: chain J residue 395 SER Chi-restraints excluded: chain J residue 416 TRP Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain K residue 355 LEU Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 296 GLU Chi-restraints excluded: chain L residue 330 ILE Chi-restraints excluded: chain L residue 429 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: [252, 347, 385, 369, 271, 10, 67, 136, 364, 392, 259] chunk 252 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 385 optimal weight: 0.0050 chunk 369 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 364 optimal weight: 5.9990 chunk 392 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN ** D 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1064 ASN ** G 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.064772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.045947 restraints weight = 102642.710| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 3.38 r_work: 0.2544 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 : 0.004 0.081 34401 Z= 0.154 Angle : 0.483 9.138 46998 Z= 0.258 Chirality : 0.043 0.164 5316 Planarity : 0.004 0.051 6189 Dihedral : 3.933 39.452 4968 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.80 % Allowed : 22.42 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 1.20 (0.12), residues: 4632 helix: 3.57 (0.15), residues: 1116 sheet: 0.34 (0.17), residues: 933 loop : -0.27 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 369 TYR 0.013 0.001 TYR G 60 PHE 0.013 0.001 PHE L 423 TRP 0.010 0.001 TRP D 103 HIS 0.007 0.001 HIS H 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (34401) covalent geometry : angle 0.48307 / 0.26 (46998) hydrogen bonds : bond 0.06047 / 4.24 ( 1517) hydrogen bonds : angle 4.31750 / 3.08 ( 4587) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 263 time to evaluate : 1.317 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: B 272 TRP cc_start: 0.7905 (OUTLIER) cc_final: 0.6367 (t60) REVERT: B 346 LEU cc_start: 0.9259 (tt) cc_final: 0.8587 (tt) REVERT: B 404 GLU cc_start: 0.8935 (mp0) cc_final: 0.8435 (mp0) REVERT: B 416 TRP cc_start: 0.8344 (OUTLIER) cc_final: 0.7359 (p-90) REVERT: C 180 MET cc_start: 0.8907 (mmm) cc_final: 0.8263 (mtt) REVERT: C 320 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8326 (mt-10) REVERT: C 332 ARG cc_start: 0.8554 (tpp80) cc_final: 0.8318 (tpp80) REVERT: D 278 MET cc_start: 0.8846 (mmm) cc_final: 0.8604 (mtm) REVERT: D 404 GLU cc_start: 0.8818 (mp0) cc_final: 0.7880 (mp0) REVERT: F 272 TRP cc_start: 0.7876 (OUTLIER) cc_final: 0.6653 (t60) REVERT: F 296 GLU cc_start: 0.9100 (tp30) cc_final: 0.8817 (mm-30) REVERT: F 346 LEU cc_start: 0.9276 (tt) cc_final: 0.8747 (tt) REVERT: F 404 GLU cc_start: 0.8758 (mp0) cc_final: 0.8294 (mp0) REVERT: F 416 TRP cc_start: 0.8083 (OUTLIER) cc_final: 0.6776 (p-90) REVERT: G 42 TRP cc_start: 0.9322 (OUTLIER) cc_final: 0.9015 (m-10) REVERT: G 320 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8689 (mt-10) REVERT: G 353 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8200 (mmp80) REVERT: H 278 MET cc_start: 0.8885 (mmm) cc_final: 0.8607 (mmm) REVERT: H 335 GLU cc_start: 0.8803 (tp30) cc_final: 0.8498 (tp30) REVERT: J 216 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7279 (pttp) REVERT: J 278 MET cc_start: 0.7982 (pmm) cc_final: 0.7771 (pmm) REVERT: J 404 GLU cc_start: 0.8767 (mp0) cc_final: 0.8286 (mp0) REVERT: J 416 TRP cc_start: 0.8192 (OUTLIER) cc_final: 0.7126 (p-90) outliers start: 94 outliers final: 69 residues processed: 343 average time/residue: 0.1872 time to fit residues: 111.0250 Evaluate side-chains 336 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 259 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain E residue 1056 THR Chi-restraints excluded: chain E residue 1061 THR Chi-restraints excluded: chain E residue 1064 ASN Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 353 ARG Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 257 ILE Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain I residue 993 LEU Chi-restraints excluded: chain I residue 1056 THR Chi-restraints excluded: chain I residue 1061 THR Chi-restraints excluded: chain I residue 1070 THR Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 272 TRP Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 379 THR Chi-restraints excluded: chain J residue 395 SER Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 416 TRP Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain K residue 355 LEU Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 245 SER Chi-restraints excluded: chain L residue 330 ILE Chi-restraints excluded: chain L residue 429 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: [140, 453, 45, 5, 313, 66, 248, 329, 100, 129, 358] chunk 140 optimal weight: 6.9990 chunk 453 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 313 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 358 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN ** D 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1064 ASN ** G 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 GLN ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.061693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.042857 restraints weight = 105663.183| |-----------------------------------------------------------------------------| r_work (start): 0.2565 rms_B_bonded: 3.35 r_work: 0.2432 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 34401 Z= 0.379 Angle : 0.644 8.271 46998 Z= 0.344 Chirality : 0.048 0.165 5316 Planarity : 0.005 0.054 6189 Dihedral : 4.454 38.085 4968 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.61 % Allowed : 21.91 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.72 (0.12), residues: 4632 helix: 3.10 (0.15), residues: 1116 sheet: 0.07 (0.17), residues: 936 loop : -0.55 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 964 TYR 0.014 0.002 TYR F 78 PHE 0.018 0.002 PHE H 423 TRP 0.026 0.002 TRP C 361 HIS 0.007 0.002 HIS F 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00886 / 0.38 (34401) covalent geometry : angle 0.64441 / 0.34 (46998) hydrogen bonds : bond 0.07127 / 5.00 ( 1517) hydrogen bonds : angle 4.78047 / 3.44 ( 4587) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 257 time to evaluate : 1.274 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: B 272 TRP cc_start: 0.7838 (OUTLIER) cc_final: 0.6277 (t60) REVERT: B 346 LEU cc_start: 0.9310 (tt) cc_final: 0.8647 (tt) REVERT: B 404 GLU cc_start: 0.9007 (mp0) cc_final: 0.8533 (mp0) REVERT: C 19 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8658 (p) REVERT: C 180 MET cc_start: 0.8985 (mmm) cc_final: 0.8329 (mtt) REVERT: C 296 GLU cc_start: 0.8891 (tp30) cc_final: 0.8645 (tp30) REVERT: C 320 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8347 (mt-10) REVERT: D 401 THR cc_start: 0.8995 (p) cc_final: 0.8048 (p) REVERT: D 404 GLU cc_start: 0.8832 (mp0) cc_final: 0.7926 (mp0) REVERT: E 1055 ASP cc_start: 0.9120 (m-30) cc_final: 0.8678 (m-30) REVERT: F 272 TRP cc_start: 0.7881 (OUTLIER) cc_final: 0.6895 (t60) REVERT: F 404 GLU cc_start: 0.8841 (mp0) cc_final: 0.8393 (mp0) REVERT: G 42 TRP cc_start: 0.9374 (OUTLIER) cc_final: 0.8993 (m-10) REVERT: G 320 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8700 (mt-10) REVERT: G 353 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8273 (mmp80) REVERT: G 416 TRP cc_start: 0.8018 (m100) cc_final: 0.7698 (m100) REVERT: H 180 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8479 (ptm) REVERT: H 278 MET cc_start: 0.8865 (mmm) cc_final: 0.8616 (mmm) REVERT: J 150 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7948 (tt) REVERT: J 216 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7449 (pttp) REVERT: J 404 GLU cc_start: 0.8769 (mp0) cc_final: 0.8287 (mp0) REVERT: K 242 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7092 (mtp) REVERT: K 320 GLU cc_start: 0.8675 (mt-10) cc_final: 0.7786 (pt0) outliers start: 121 outliers final: 90 residues processed: 362 average time/residue: 0.1831 time to fit residues: 114.4032 Evaluate side-chains 349 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 250 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain E residue 999 ASP Chi-restraints excluded: chain E residue 1029 ILE Chi-restraints excluded: chain E residue 1056 THR Chi-restraints excluded: chain E residue 1061 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 353 ARG Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 180 MET Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 257 ILE Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain I residue 929 GLU Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain I residue 999 ASP Chi-restraints excluded: chain I residue 1056 THR Chi-restraints excluded: chain I residue 1061 THR Chi-restraints excluded: chain I residue 1070 THR Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 272 TRP Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 379 THR Chi-restraints excluded: chain J residue 395 SER Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 416 TRP Chi-restraints excluded: chain J residue 448 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 241 LEU Chi-restraints excluded: chain K residue 242 MET Chi-restraints excluded: chain K residue 258 THR Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain K residue 355 LEU Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 229 THR Chi-restraints excluded: chain L residue 245 SER Chi-restraints excluded: chain L residue 257 ILE Chi-restraints excluded: chain L residue 296 GLU Chi-restraints excluded: chain L residue 429 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: [446, 127, 373, 203, 94, 42, 376, 299, 163, 357, 201] chunk 446 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 373 optimal weight: 0.5980 chunk 203 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 376 optimal weight: 0.9980 chunk 299 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 357 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1064 ASN ** G 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 200 GLN ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.045905 restraints weight = 102423.317| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.36 r_work: 0.2510 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34401 Z= 0.124 Angle : 0.486 8.091 46998 Z= 0.262 Chirality : 0.042 0.162 5316 Planarity : 0.004 0.055 6189 Dihedral : 4.066 38.794 4968 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.36 % Allowed : 23.17 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 1.09 (0.12), residues: 4632 helix: 3.52 (0.15), residues: 1116 sheet: 0.19 (0.17), residues: 936 loop : -0.33 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 949 TYR 0.011 0.001 TYR G 60 PHE 0.010 0.001 PHE L 423 TRP 0.021 0.001 TRP C 361 HIS 0.008 0.001 HIS D 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (34401) covalent geometry : angle 0.48632 / 0.26 (46998) hydrogen bonds : bond 0.06056 / 4.25 ( 1517) hydrogen bonds : angle 4.33221 / 3.09 ( 4587) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 264 time to evaluate : 1.204 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: B 272 TRP cc_start: 0.7945 (OUTLIER) cc_final: 0.6320 (t60) REVERT: B 346 LEU cc_start: 0.9323 (tt) cc_final: 0.8619 (tt) REVERT: B 404 GLU cc_start: 0.8934 (mp0) cc_final: 0.8457 (mp0) REVERT: C 19 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8702 (p) REVERT: C 180 MET cc_start: 0.8931 (mmm) cc_final: 0.8299 (mtt) REVERT: C 242 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6817 (mtp) REVERT: C 296 GLU cc_start: 0.8882 (tp30) cc_final: 0.8645 (tp30) REVERT: C 320 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8344 (mt-10) REVERT: D 278 MET cc_start: 0.8847 (mmm) cc_final: 0.8606 (mtm) REVERT: D 404 GLU cc_start: 0.8832 (mp0) cc_final: 0.7910 (mp0) REVERT: E 1055 ASP cc_start: 0.9101 (m-30) cc_final: 0.8645 (m-30) REVERT: F 272 TRP cc_start: 0.7944 (OUTLIER) cc_final: 0.6698 (t60) REVERT: F 346 LEU cc_start: 0.9211 (tt) cc_final: 0.8648 (tt) REVERT: F 404 GLU cc_start: 0.8805 (mp0) cc_final: 0.8375 (mp0) REVERT: F 416 TRP cc_start: 0.8219 (OUTLIER) cc_final: 0.6713 (p-90) REVERT: G 42 TRP cc_start: 0.9357 (OUTLIER) cc_final: 0.9023 (m-10) REVERT: G 306 GLN cc_start: 0.9591 (tt0) cc_final: 0.9325 (pt0) REVERT: H 180 MET cc_start: 0.8652 (ptm) cc_final: 0.8391 (ptm) REVERT: H 278 MET cc_start: 0.8862 (mmm) cc_final: 0.8586 (mmm) REVERT: J 150 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7951 (tt) REVERT: J 216 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7379 (pttp) REVERT: J 404 GLU cc_start: 0.8781 (mp0) cc_final: 0.8319 (mp0) REVERT: J 416 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.7119 (p-90) REVERT: K 242 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6942 (mtp) REVERT: K 296 GLU cc_start: 0.8971 (tp30) cc_final: 0.8616 (tp30) REVERT: K 320 GLU cc_start: 0.8697 (mt-10) cc_final: 0.7899 (pt0) outliers start: 79 outliers final: 59 residues processed: 326 average time/residue: 0.1812 time to fit residues: 101.5277 Evaluate side-chains 328 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 259 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain E residue 1029 ILE Chi-restraints excluded: chain E residue 1064 ASN Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 272 TRP Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 379 THR Chi-restraints excluded: chain J residue 395 SER Chi-restraints excluded: chain J residue 416 TRP Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 242 MET Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain K residue 355 LEU Chi-restraints excluded: chain K residue 364 VAL Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 245 SER Chi-restraints excluded: chain L residue 296 GLU Chi-restraints excluded: chain L residue 429 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: [170, 369, 125, 130, 428, 460, 216, 426, 223, 442, 308] chunk 170 optimal weight: 0.8980 chunk 369 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 130 optimal weight: 0.4980 chunk 428 optimal weight: 0.9980 chunk 460 optimal weight: 0.0970 chunk 216 optimal weight: 3.9990 chunk 426 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 442 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 ASN ** L 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.065552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.046751 restraints weight = 101887.567| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 3.36 r_work: 0.2549 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 34401 Z= 0.114 Angle : 0.479 9.441 46998 Z= 0.255 Chirality : 0.042 0.163 5316 Planarity : 0.004 0.056 6189 Dihedral : 3.858 40.424 4968 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.18 % Allowed : 23.43 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 1.27 (0.13), residues: 4632 helix: 3.67 (0.15), residues: 1116 sheet: 0.15 (0.16), residues: 966 loop : -0.14 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 214 TYR 0.008 0.001 TYR G 60 PHE 0.011 0.001 PHE C 423 TRP 0.023 0.001 TRP G 416 HIS 0.009 0.001 HIS D 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (34401) covalent geometry : angle 0.47906 / 0.25 (46998) hydrogen bonds : bond 0.05794 / 4.07 ( 1517) hydrogen bonds : angle 4.19594 / 2.99 ( 4587) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 269 time to evaluate : 1.205 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: B 272 TRP cc_start: 0.8044 (OUTLIER) cc_final: 0.6543 (t60) REVERT: B 296 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8806 (mm-30) REVERT: B 346 LEU cc_start: 0.9283 (tt) cc_final: 0.8563 (tt) REVERT: B 404 GLU cc_start: 0.8872 (mp0) cc_final: 0.8384 (mp0) REVERT: B 416 TRP cc_start: 0.8571 (OUTLIER) cc_final: 0.7543 (p-90) REVERT: C 19 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8738 (p) REVERT: C 180 MET cc_start: 0.8876 (mmm) cc_final: 0.8335 (mtt) REVERT: C 242 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6869 (mtp) REVERT: C 320 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8349 (mt-10) REVERT: D 278 MET cc_start: 0.8839 (mmm) cc_final: 0.8615 (mtm) REVERT: D 404 GLU cc_start: 0.8824 (mp0) cc_final: 0.7884 (mp0) REVERT: E 1055 ASP cc_start: 0.9127 (m-30) cc_final: 0.8657 (m-30) REVERT: F 272 TRP cc_start: 0.8001 (OUTLIER) cc_final: 0.6698 (t60) REVERT: F 346 LEU cc_start: 0.9208 (tt) cc_final: 0.8634 (tt) REVERT: F 404 GLU cc_start: 0.8736 (mp0) cc_final: 0.8301 (mp0) REVERT: F 416 TRP cc_start: 0.7928 (OUTLIER) cc_final: 0.6635 (p-90) REVERT: G 42 TRP cc_start: 0.9326 (OUTLIER) cc_final: 0.9007 (m-10) REVERT: G 242 MET cc_start: 0.7342 (ttp) cc_final: 0.6368 (ptm) REVERT: G 306 GLN cc_start: 0.9605 (tt0) cc_final: 0.9344 (pt0) REVERT: G 353 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8337 (mmp80) REVERT: H 278 MET cc_start: 0.8835 (mmm) cc_final: 0.8573 (mmm) REVERT: J 150 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8013 (tt) REVERT: J 216 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7354 (pttp) REVERT: J 404 GLU cc_start: 0.8763 (mp0) cc_final: 0.8287 (mp0) REVERT: J 416 TRP cc_start: 0.8002 (OUTLIER) cc_final: 0.6949 (p-90) REVERT: K 242 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6966 (mtp) REVERT: K 320 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8063 (pt0) outliers start: 73 outliers final: 47 residues processed: 326 average time/residue: 0.1953 time to fit residues: 108.4708 Evaluate side-chains 321 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 261 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain E residue 1056 THR Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 353 ARG Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain I residue 1070 THR Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 395 SER Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 416 TRP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 241 LEU Chi-restraints excluded: chain K residue 242 MET Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain K residue 355 LEU Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 245 SER Chi-restraints excluded: chain L residue 257 ILE Chi-restraints excluded: chain L residue 296 GLU Chi-restraints excluded: chain L residue 429 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: [294, 306, 236, 375, 427, 396, 325, 211, 301, 246, 63] chunk 294 optimal weight: 5.9990 chunk 306 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 375 optimal weight: 3.9990 chunk 427 optimal weight: 3.9990 chunk 396 optimal weight: 8.9990 chunk 325 optimal weight: 1.9990 chunk 211 optimal weight: 0.3980 chunk 301 optimal weight: 7.9990 chunk 246 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN ** D 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.063997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.045221 restraints weight = 103642.858| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 3.37 r_work: 0.2494 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34401 Z= 0.189 Angle : 0.520 11.863 46998 Z= 0.274 Chirality : 0.043 0.162 5316 Planarity : 0.004 0.056 6189 Dihedral : 3.979 40.456 4968 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.18 % Allowed : 23.23 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 1.19 (0.12), residues: 4632 helix: 3.59 (0.15), residues: 1116 sheet: 0.23 (0.17), residues: 936 loop : -0.25 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 214 TYR 0.008 0.001 TYR L 146 PHE 0.013 0.001 PHE L 423 TRP 0.013 0.001 TRP D 416 HIS 0.008 0.001 HIS D 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (34401) covalent geometry : angle 0.52009 / 0.27 (46998) hydrogen bonds : bond 0.06147 / 4.32 ( 1517) hydrogen bonds : angle 4.31087 / 3.08 ( 4587) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 260 time to evaluate : 1.346 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: B 272 TRP cc_start: 0.8013 (OUTLIER) cc_final: 0.6504 (t60) REVERT: B 296 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8705 (mm-30) REVERT: B 346 LEU cc_start: 0.9285 (tt) cc_final: 0.8536 (tt) REVERT: B 348 MET cc_start: 0.8698 (ttt) cc_final: 0.7944 (tpp) REVERT: B 404 GLU cc_start: 0.8870 (mp0) cc_final: 0.8366 (mp0) REVERT: B 416 TRP cc_start: 0.8611 (OUTLIER) cc_final: 0.7629 (p-90) REVERT: C 19 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8654 (p) REVERT: C 180 MET cc_start: 0.8927 (mmm) cc_final: 0.8367 (mtt) REVERT: C 242 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7088 (mtp) REVERT: C 320 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8335 (mt-10) REVERT: C 360 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8263 (mp10) REVERT: D 278 MET cc_start: 0.8834 (mmm) cc_final: 0.8609 (mtm) REVERT: D 404 GLU cc_start: 0.8822 (mp0) cc_final: 0.7882 (mp0) REVERT: E 1055 ASP cc_start: 0.9137 (m-30) cc_final: 0.8664 (m-30) REVERT: F 272 TRP cc_start: 0.8004 (OUTLIER) cc_final: 0.6744 (t60) REVERT: F 346 LEU cc_start: 0.9234 (tt) cc_final: 0.8690 (tt) REVERT: F 404 GLU cc_start: 0.8769 (mp0) cc_final: 0.8344 (mp0) REVERT: F 416 TRP cc_start: 0.8178 (OUTLIER) cc_final: 0.6872 (p-90) REVERT: G 42 TRP cc_start: 0.9339 (OUTLIER) cc_final: 0.8950 (m-10) REVERT: G 306 GLN cc_start: 0.9604 (tt0) cc_final: 0.9338 (pt0) REVERT: G 320 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8050 (pt0) REVERT: G 353 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8329 (mmp80) REVERT: H 278 MET cc_start: 0.8850 (mmm) cc_final: 0.8599 (mmm) REVERT: J 150 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7967 (tt) REVERT: J 180 MET cc_start: 0.8088 (mtt) cc_final: 0.7711 (mtt) REVERT: J 216 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7366 (pttp) REVERT: J 404 GLU cc_start: 0.8747 (mp0) cc_final: 0.8288 (mp0) REVERT: J 416 TRP cc_start: 0.8434 (OUTLIER) cc_final: 0.7281 (p-90) REVERT: K 242 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7061 (mtp) REVERT: K 320 GLU cc_start: 0.8687 (mt-10) cc_final: 0.7865 (pt0) REVERT: K 375 MET cc_start: 0.9176 (ttp) cc_final: 0.8796 (tmm) outliers start: 73 outliers final: 54 residues processed: 316 average time/residue: 0.1937 time to fit residues: 105.0676 Evaluate side-chains 326 residues out of total 3354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 258 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1029 ILE Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 272 TRP Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 984 GLU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 272 TRP Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 379 THR Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain G residue 42 TRP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 353 ARG Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 245 SER Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain I residue 984 GLU Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 216 LYS Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 379 THR Chi-restraints excluded: chain J residue 395 SER Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 416 TRP Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 241 LEU Chi-restraints excluded: chain K residue 242 MET Chi-restraints excluded: chain K residue 352 SER Chi-restraints excluded: chain K residue 355 LEU Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 229 THR Chi-restraints excluded: chain L residue 245 SER Chi-restraints excluded: chain L residue 257 ILE Chi-restraints excluded: chain L residue 296 GLU Chi-restraints excluded: chain L residue 429 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: [388, 302, 91, 322, 289, 414, 100, 192, 398, 407, 74] chunk 388 optimal weight: 5.9990 chunk 302 optimal weight: 0.0070 chunk 91 optimal weight: 0.7980 chunk 322 optimal weight: 0.9980 chunk 289 optimal weight: 4.9990 chunk 414 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 398 optimal weight: 4.9990 chunk 407 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN ** D 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.064622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.045673 restraints weight = 105687.622| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 3.25 r_work: 0.2575 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 34401 Z= 0.188 Angle : 0.638 59.159 46998 Z= 0.354 Chirality : 0.043 0.218 5316 Planarity : 0.004 0.056 6189 Dihedral : 3.978 40.429 4968 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.21 % Allowed : 23.23 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 1.19 (0.12), residues: 4632 helix: 3.59 (0.15), residues: 1116 sheet: 0.23 (0.17), residues: 936 loop : -0.25 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 214 TYR 0.008 0.001 TYR L 146 PHE 0.012 0.001 PHE L 423 TRP 0.012 0.001 TRP D 416 HIS 0.008 0.001 HIS D 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (34401) covalent geometry : angle 0.63756 / 0.35 (46998) hydrogen bonds : bond 0.06090 / 4.28 ( 1517) hydrogen bonds : angle 4.30787 / 3.08 ( 4587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8498.50 seconds wall clock time: 145 minutes 40.22 seconds (8740.22 seconds total)