Starting phenix.real_space_refine on Tue Aug 26 16:04:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ilm_35536/08_2025/8ilm_35536_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ilm_35536/08_2025/8ilm_35536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ilm_35536/08_2025/8ilm_35536_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ilm_35536/08_2025/8ilm_35536_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ilm_35536/08_2025/8ilm_35536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ilm_35536/08_2025/8ilm_35536.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1296 atoms to isotropic. 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 217 5.16 5 C 24041 2.51 5 N 6628 2.21 5 O 7022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 321 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37908 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "B" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3557 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 21, 'TRANS': 431} Chain: "C" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 515 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "D" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1640 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1640 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain: "F" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "G" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "H" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "I" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3557 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 21, 'TRANS': 431} Chain: "J" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3557 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 21, 'TRANS': 431} Chain: "K" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3557 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 21, 'TRANS': 431} Chain: "L" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "M" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "N" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "O" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 569 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "P" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 569 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "Q" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "R" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1133 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 138} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "S" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1124 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 140} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 9.32, per 1000 atoms: 0.25 Number of scatterers: 37908 At special positions: 0 Unit cell: (189.376, 147.412, 150.64, 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 217 16.00 O 7022 8.00 N 6628 7.00 C 24041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS B 244 " distance=2.29 Simple disulfide: pdb=" SG CYS F 244 " - pdb=" SG CYS I 244 " distance=2.05 Simple disulfide: pdb=" SG CYS G 244 " - pdb=" SG CYS J 244 " distance=2.04 Simple disulfide: pdb=" SG CYS H 244 " - pdb=" SG CYS K 244 " distance=2.05 Simple disulfide: pdb=" SG CYS L 16 " - pdb=" SG CYS L 65 " distance=2.04 Simple disulfide: pdb=" SG CYS M 16 " - pdb=" SG CYS M 65 " distance=2.04 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 65 " distance=2.02 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 65 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8784 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 36 sheets defined 40.6% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 109 through 118 removed outlier: 3.908A pdb=" N ILE A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 152 through 160 removed outlier: 3.854A pdb=" N LEU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.819A pdb=" N GLY A 193 " --> pdb=" O CYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 removed outlier: 3.611A pdb=" N ARG A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.721A pdb=" N ASN A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 4.045A pdb=" N LEU A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.727A pdb=" N GLU A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 4.214A pdb=" N LEU A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 405' Processing helix chain 'A' and resid 410 through 430 removed outlier: 3.799A pdb=" N GLU A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 446 removed outlier: 3.623A pdb=" N ILE A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.595A pdb=" N LEU A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 58 Processing helix chain 'B' and resid 101 through 105 removed outlier: 4.086A pdb=" N LEU B 104 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 105 " --> pdb=" O LEU B 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 101 through 105' Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.961A pdb=" N ILE B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 152 through 160 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 211 through 230 removed outlier: 4.095A pdb=" N PHE B 217 " --> pdb=" O ASP B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 258 removed outlier: 3.676A pdb=" N GLY B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 removed outlier: 3.647A pdb=" N ASN B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.905A pdb=" N LEU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 348 removed outlier: 3.935A pdb=" N THR B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 400 through 405 removed outlier: 3.724A pdb=" N LEU B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 removed outlier: 3.506A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 447 removed outlier: 3.685A pdb=" N GLU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLY B 439 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASP B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 447 " --> pdb=" O ARG B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 459 Processing helix chain 'D' and resid 23 through 33 Processing helix chain 'D' and resid 37 through 49 Proline residue: D 43 - end of helix Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 65 through 84 Processing helix chain 'D' and resid 88 through 93 removed outlier: 4.607A pdb=" N ILE D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 105 through 109 removed outlier: 4.211A pdb=" N LEU D 108 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 124 removed outlier: 4.138A pdb=" N VAL D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 141 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 157 through 172 Processing helix chain 'D' and resid 179 through 189 removed outlier: 3.929A pdb=" N MET D 183 " --> pdb=" O GLN D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'E' and resid 23 through 33 Processing helix chain 'E' and resid 37 through 49 Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 54 through 62 Processing helix chain 'E' and resid 65 through 84 Processing helix chain 'E' and resid 88 through 93 removed outlier: 4.608A pdb=" N ILE E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 104 Processing helix chain 'E' and resid 105 through 109 removed outlier: 4.210A pdb=" N LEU E 108 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 124 removed outlier: 4.137A pdb=" N VAL E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA E 116 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR E 119 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 141 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 157 through 172 Processing helix chain 'E' and resid 179 through 189 removed outlier: 3.928A pdb=" N MET E 183 " --> pdb=" O GLN E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 205 Processing helix chain 'F' and resid 17 through 21 removed outlier: 3.547A pdb=" N THR F 20 " --> pdb=" O TYR F 17 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR F 21 " --> pdb=" O LYS F 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 17 through 21' Processing helix chain 'F' and resid 46 through 58 removed outlier: 3.536A pdb=" N SER F 58 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 78 removed outlier: 4.277A pdb=" N LYS F 78 " --> pdb=" O ASP F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 119 removed outlier: 3.837A pdb=" N ILE F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.651A pdb=" N GLY F 123 " --> pdb=" O ASN F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 143 Processing helix chain 'F' and resid 152 through 160 Processing helix chain 'F' and resid 180 through 193 removed outlier: 3.842A pdb=" N GLY F 193 " --> pdb=" O CYS F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 230 removed outlier: 3.618A pdb=" N ARG F 214 " --> pdb=" O ARG F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 257 Processing helix chain 'F' and resid 270 through 285 removed outlier: 3.690A pdb=" N ASN F 274 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 319 removed outlier: 3.997A pdb=" N LEU F 311 " --> pdb=" O HIS F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 345 removed outlier: 3.834A pdb=" N SER F 338 " --> pdb=" O GLY F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 382 No H-bonds generated for 'chain 'F' and resid 380 through 382' Processing helix chain 'F' and resid 383 through 391 Processing helix chain 'F' and resid 400 through 405 removed outlier: 3.865A pdb=" N LEU F 404 " --> pdb=" O GLY F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 429 Processing helix chain 'F' and resid 437 through 446 Processing helix chain 'F' and resid 449 through 459 Processing helix chain 'G' and resid 46 through 58 removed outlier: 3.868A pdb=" N ALA G 50 " --> pdb=" O PRO G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 removed outlier: 3.908A pdb=" N ILE G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 143 Processing helix chain 'G' and resid 152 through 160 removed outlier: 3.855A pdb=" N LEU G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 3.679A pdb=" N GLY G 193 " --> pdb=" O CYS G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 230 removed outlier: 3.611A pdb=" N ARG G 214 " --> pdb=" O ARG G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 257 Processing helix chain 'G' and resid 270 through 285 removed outlier: 3.721A pdb=" N ASN G 274 " --> pdb=" O GLY G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 319 removed outlier: 4.044A pdb=" N LEU G 311 " --> pdb=" O HIS G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 345 Processing helix chain 'G' and resid 354 through 358 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 392 removed outlier: 3.803A pdb=" N GLU G 389 " --> pdb=" O PRO G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 405 removed outlier: 4.213A pdb=" N LEU G 404 " --> pdb=" O GLY G 400 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY G 405 " --> pdb=" O GLY G 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 400 through 405' Processing helix chain 'G' and resid 410 through 430 removed outlier: 3.764A pdb=" N GLU G 430 " --> pdb=" O GLN G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 446 removed outlier: 3.623A pdb=" N ILE G 441 " --> pdb=" O GLU G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 459 Processing helix chain 'H' and resid 47 through 58 removed outlier: 3.537A pdb=" N SER H 58 " --> pdb=" O ILE H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 118 removed outlier: 3.853A pdb=" N ILE H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 143 Processing helix chain 'H' and resid 152 through 160 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.705A pdb=" N GLY H 193 " --> pdb=" O CYS H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 230 removed outlier: 3.655A pdb=" N ARG H 214 " --> pdb=" O ARG H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 257 Processing helix chain 'H' and resid 270 through 285 removed outlier: 3.731A pdb=" N ASN H 274 " --> pdb=" O GLY H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 319 removed outlier: 4.046A pdb=" N LEU H 311 " --> pdb=" O HIS H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 345 removed outlier: 3.588A pdb=" N ALA H 337 " --> pdb=" O GLU H 333 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER H 338 " --> pdb=" O GLY H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 358 Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 391 Processing helix chain 'H' and resid 400 through 405 removed outlier: 4.303A pdb=" N LEU H 404 " --> pdb=" O GLY H 400 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY H 405 " --> pdb=" O GLY H 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 400 through 405' Processing helix chain 'H' and resid 410 through 430 removed outlier: 3.576A pdb=" N GLU H 430 " --> pdb=" O GLN H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 446 Processing helix chain 'H' and resid 449 through 459 Processing helix chain 'I' and resid 47 through 59 Processing helix chain 'I' and resid 101 through 105 removed outlier: 3.959A pdb=" N LEU I 104 " --> pdb=" O PRO I 101 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE I 105 " --> pdb=" O LEU I 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 101 through 105' Processing helix chain 'I' and resid 109 through 118 removed outlier: 3.910A pdb=" N ILE I 113 " --> pdb=" O SER I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 124 Processing helix chain 'I' and resid 138 through 143 Processing helix chain 'I' and resid 152 through 160 removed outlier: 3.784A pdb=" N LEU I 159 " --> pdb=" O GLU I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 193 removed outlier: 3.824A pdb=" N GLY I 193 " --> pdb=" O CYS I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 230 removed outlier: 3.626A pdb=" N ARG I 214 " --> pdb=" O ARG I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 243 through 257 Processing helix chain 'I' and resid 270 through 285 removed outlier: 3.632A pdb=" N ASN I 274 " --> pdb=" O GLY I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 300 removed outlier: 3.623A pdb=" N ARG I 300 " --> pdb=" O ALA I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 319 removed outlier: 3.848A pdb=" N LEU I 311 " --> pdb=" O HIS I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 346 removed outlier: 3.969A pdb=" N SER I 338 " --> pdb=" O GLY I 334 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 358 Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 391 Processing helix chain 'I' and resid 400 through 405 removed outlier: 3.756A pdb=" N LEU I 404 " --> pdb=" O GLY I 400 " (cutoff:3.500A) Processing helix chain 'I' and resid 410 through 430 removed outlier: 3.572A pdb=" N GLU I 430 " --> pdb=" O GLN I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 437 through 447 Processing helix chain 'I' and resid 449 through 459 removed outlier: 3.612A pdb=" N TRP I 459 " --> pdb=" O ALA I 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 58 Processing helix chain 'J' and resid 101 through 105 removed outlier: 4.087A pdb=" N LEU J 104 " --> pdb=" O PRO J 101 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE J 105 " --> pdb=" O LEU J 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 101 through 105' Processing helix chain 'J' and resid 109 through 118 removed outlier: 3.962A pdb=" N ILE J 113 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 124 Processing helix chain 'J' and resid 138 through 143 Processing helix chain 'J' and resid 152 through 160 Processing helix chain 'J' and resid 178 through 193 removed outlier: 3.788A pdb=" N GLY J 193 " --> pdb=" O CYS J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 230 removed outlier: 4.095A pdb=" N PHE J 217 " --> pdb=" O ASP J 213 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA J 227 " --> pdb=" O HIS J 223 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU J 228 " --> pdb=" O LYS J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 258 removed outlier: 3.676A pdb=" N GLY J 258 " --> pdb=" O ALA J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 284 removed outlier: 3.647A pdb=" N ASN J 274 " --> pdb=" O GLY J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 319 removed outlier: 3.905A pdb=" N LEU J 311 " --> pdb=" O HIS J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 348 removed outlier: 3.935A pdb=" N THR J 339 " --> pdb=" O ASP J 335 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU J 345 " --> pdb=" O GLY J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 354 through 358 Processing helix chain 'J' and resid 380 through 382 No H-bonds generated for 'chain 'J' and resid 380 through 382' Processing helix chain 'J' and resid 383 through 391 Processing helix chain 'J' and resid 400 through 405 removed outlier: 3.736A pdb=" N LEU J 404 " --> pdb=" O GLY J 400 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 431 Processing helix chain 'J' and resid 433 through 446 removed outlier: 5.418A pdb=" N GLY J 439 " --> pdb=" O TYR J 435 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASP J 440 " --> pdb=" O ARG J 436 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 459 Processing helix chain 'K' and resid 46 through 58 removed outlier: 3.807A pdb=" N ALA K 50 " --> pdb=" O PRO K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 105 removed outlier: 4.079A pdb=" N LEU K 104 " --> pdb=" O PRO K 101 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE K 105 " --> pdb=" O LEU K 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 101 through 105' Processing helix chain 'K' and resid 109 through 118 removed outlier: 3.955A pdb=" N ILE K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 124 Processing helix chain 'K' and resid 138 through 143 Processing helix chain 'K' and resid 152 through 160 Processing helix chain 'K' and resid 178 through 193 removed outlier: 3.843A pdb=" N GLY K 193 " --> pdb=" O CYS K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 230 removed outlier: 4.296A pdb=" N PHE K 217 " --> pdb=" O ASP K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 258 removed outlier: 3.682A pdb=" N GLY K 258 " --> pdb=" O ALA K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 285 removed outlier: 3.665A pdb=" N ASN K 274 " --> pdb=" O GLY K 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 300 removed outlier: 3.547A pdb=" N ARG K 300 " --> pdb=" O ALA K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 319 removed outlier: 3.876A pdb=" N LEU K 311 " --> pdb=" O HIS K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 348 Processing helix chain 'K' and resid 354 through 358 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 391 Processing helix chain 'K' and resid 400 through 405 removed outlier: 3.692A pdb=" N LEU K 404 " --> pdb=" O GLY K 400 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 430 removed outlier: 3.524A pdb=" N GLU K 430 " --> pdb=" O GLN K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 437 through 446 Processing helix chain 'K' and resid 449 through 459 Processing helix chain 'R' and resid 315 through 322 removed outlier: 3.653A pdb=" N ILE R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 350 through 357 removed outlier: 4.218A pdb=" N GLY R 357 " --> pdb=" O VAL R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 412 through 418 Processing helix chain 'S' and resid 315 through 322 removed outlier: 3.604A pdb=" N ILE S 319 " --> pdb=" O GLY S 315 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 357 removed outlier: 3.552A pdb=" N ILE S 356 " --> pdb=" O PRO S 352 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY S 357 " --> pdb=" O VAL S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 367 through 372 removed outlier: 4.262A pdb=" N VAL S 371 " --> pdb=" O ASP S 367 " (cutoff:3.500A) Processing helix chain 'S' and resid 388 through 390 No H-bonds generated for 'chain 'S' and resid 388 through 390' Processing helix chain 'S' and resid 412 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 86 removed outlier: 5.670A pdb=" N CYS A 81 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA A 99 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 34 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE A 135 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA A 36 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N GLY A 305 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU A 130 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 198 removed outlier: 6.966A pdb=" N LEU A 167 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LYS A 198 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS A 169 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N MET A 166 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A 324 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 262 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N HIS A 291 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N HIS A 264 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 237 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ASP A 265 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.040A pdb=" N CYS B 81 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA B 99 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS B 83 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 34 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE B 135 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA B 36 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N GLY B 305 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 130 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 166 through 170 removed outlier: 6.580A pdb=" N LEU B 167 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LYS B 198 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS B 169 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR B 197 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ASN B 238 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS B 235 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N MET B 263 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU B 237 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ASP B 265 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 262 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N HIS B 291 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N HIS B 264 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B 324 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLN B 398 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA B 375 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AA8, first strand: chain 'F' and resid 80 through 86 removed outlier: 5.991A pdb=" N CYS F 81 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA F 99 " --> pdb=" O CYS F 81 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS F 83 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU F 34 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE F 135 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA F 36 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N GLY F 305 " --> pdb=" O ARG F 128 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU F 130 " --> pdb=" O GLY F 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 166 through 170 removed outlier: 6.683A pdb=" N LEU F 167 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LYS F 198 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N CYS F 169 " --> pdb=" O LYS F 198 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR F 197 " --> pdb=" O TYR F 236 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASN F 238 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N HIS F 235 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N MET F 263 " --> pdb=" O HIS F 235 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU F 237 " --> pdb=" O MET F 263 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASP F 265 " --> pdb=" O LEU F 237 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE F 262 " --> pdb=" O HIS F 289 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N HIS F 291 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS F 264 " --> pdb=" O HIS F 291 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS F 324 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLN F 398 " --> pdb=" O PRO F 373 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA F 375 " --> pdb=" O GLN F 398 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 350 through 351 Processing sheet with id=AB2, first strand: chain 'G' and resid 81 through 86 removed outlier: 5.670A pdb=" N CYS G 81 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA G 99 " --> pdb=" O CYS G 81 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU G 34 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE G 135 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA G 36 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLY G 305 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU G 130 " --> pdb=" O GLY G 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 196 through 198 removed outlier: 6.965A pdb=" N LEU G 167 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LYS G 198 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N CYS G 169 " --> pdb=" O LYS G 198 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N MET G 166 " --> pdb=" O LEU G 397 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS G 324 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE G 262 " --> pdb=" O HIS G 289 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N HIS G 291 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS G 264 " --> pdb=" O HIS G 291 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU G 237 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ASP G 265 " --> pdb=" O LEU G 237 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 350 through 351 Processing sheet with id=AB5, first strand: chain 'H' and resid 81 through 86 removed outlier: 5.575A pdb=" N CYS H 81 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA H 99 " --> pdb=" O CYS H 81 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU H 34 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE H 135 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA H 36 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N GLY H 305 " --> pdb=" O ARG H 128 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU H 130 " --> pdb=" O GLY H 305 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 196 through 198 removed outlier: 6.968A pdb=" N LEU H 167 " --> pdb=" O PHE H 196 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LYS H 198 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS H 169 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET H 166 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS H 324 " --> pdb=" O ILE H 290 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU H 237 " --> pdb=" O MET H 263 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 350 through 351 Processing sheet with id=AB8, first strand: chain 'I' and resid 80 through 83 removed outlier: 6.017A pdb=" N CYS I 81 " --> pdb=" O ALA I 99 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA I 99 " --> pdb=" O CYS I 81 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS I 83 " --> pdb=" O PHE I 97 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU I 34 " --> pdb=" O ILE I 135 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE I 135 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA I 36 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 166 through 170 removed outlier: 7.207A pdb=" N THR I 197 " --> pdb=" O TYR I 236 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ASN I 238 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N HIS I 235 " --> pdb=" O ILE I 261 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N MET I 263 " --> pdb=" O HIS I 235 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU I 237 " --> pdb=" O MET I 263 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ASP I 265 " --> pdb=" O LEU I 237 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLN I 398 " --> pdb=" O PRO I 373 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA I 375 " --> pdb=" O GLN I 398 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 350 through 351 Processing sheet with id=AC2, first strand: chain 'J' and resid 80 through 83 removed outlier: 6.040A pdb=" N CYS J 81 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA J 99 " --> pdb=" O CYS J 81 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS J 83 " --> pdb=" O PHE J 97 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU J 34 " --> pdb=" O ILE J 135 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE J 135 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA J 36 " --> pdb=" O GLU J 133 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N GLY J 305 " --> pdb=" O ARG J 128 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU J 130 " --> pdb=" O GLY J 305 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 166 through 170 removed outlier: 6.580A pdb=" N LEU J 167 " --> pdb=" O PHE J 196 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LYS J 198 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS J 169 " --> pdb=" O LYS J 198 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR J 197 " --> pdb=" O TYR J 236 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ASN J 238 " --> pdb=" O THR J 197 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS J 235 " --> pdb=" O ILE J 261 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N MET J 263 " --> pdb=" O HIS J 235 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU J 237 " --> pdb=" O MET J 263 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ASP J 265 " --> pdb=" O LEU J 237 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE J 262 " --> pdb=" O HIS J 289 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N HIS J 291 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N HIS J 264 " --> pdb=" O HIS J 291 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS J 324 " --> pdb=" O ILE J 290 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLN J 398 " --> pdb=" O PRO J 373 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA J 375 " --> pdb=" O GLN J 398 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 350 through 351 Processing sheet with id=AC5, first strand: chain 'K' and resid 80 through 83 removed outlier: 6.071A pdb=" N CYS K 81 " --> pdb=" O ALA K 99 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA K 99 " --> pdb=" O CYS K 81 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS K 83 " --> pdb=" O PHE K 97 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU K 34 " --> pdb=" O ILE K 135 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE K 135 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA K 36 " --> pdb=" O GLU K 133 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N GLY K 305 " --> pdb=" O ARG K 128 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU K 130 " --> pdb=" O GLY K 305 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 166 through 170 removed outlier: 6.546A pdb=" N LEU K 167 " --> pdb=" O PHE K 196 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LYS K 198 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N CYS K 169 " --> pdb=" O LYS K 198 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR K 197 " --> pdb=" O TYR K 236 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ASN K 238 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N HIS K 235 " --> pdb=" O ILE K 261 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET K 263 " --> pdb=" O HIS K 235 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU K 237 " --> pdb=" O MET K 263 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ASP K 265 " --> pdb=" O LEU K 237 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE K 262 " --> pdb=" O HIS K 289 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N HIS K 291 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N HIS K 264 " --> pdb=" O HIS K 291 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS K 324 " --> pdb=" O ILE K 290 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLN K 398 " --> pdb=" O PRO K 373 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA K 375 " --> pdb=" O GLN K 398 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 350 through 351 Processing sheet with id=AC8, first strand: chain 'L' and resid 24 through 26 Processing sheet with id=AC9, first strand: chain 'M' and resid 24 through 26 Processing sheet with id=AD1, first strand: chain 'N' and resid 24 through 26 Processing sheet with id=AD2, first strand: chain 'O' and resid 24 through 26 Processing sheet with id=AD3, first strand: chain 'P' and resid 24 through 26 Processing sheet with id=AD4, first strand: chain 'Q' and resid 24 through 26 Processing sheet with id=AD5, first strand: chain 'R' and resid 344 through 345 removed outlier: 3.721A pdb=" N GLY R 425 " --> pdb=" O LEU R 400 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR R 398 " --> pdb=" O VAL R 427 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 326 through 328 Processing sheet with id=AD7, first strand: chain 'S' and resid 290 through 292 removed outlier: 3.686A pdb=" N ARG S 432 " --> pdb=" O VAL S 291 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL S 427 " --> pdb=" O ASP S 386 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP S 386 " --> pdb=" O VAL S 427 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU S 429 " --> pdb=" O VAL S 384 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY S 360 " --> pdb=" O VAL S 306 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 290 through 292 removed outlier: 3.686A pdb=" N ARG S 432 " --> pdb=" O VAL S 291 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY S 425 " --> pdb=" O LEU S 400 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR S 398 " --> pdb=" O VAL S 427 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 326 through 328 1426 hydrogen bonds defined for protein. 4080 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: 8.61 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.52: 29014 1.52 - 1.85: 9786 1.85 - 2.18: 3 2.18 - 2.51: 0 2.51 - 2.85: 1 Bond restraints: 38804 Sorted by residual: bond pdb=" C ASP R 367 " pdb=" N ARG R 369 " ideal model delta sigma weight residual 1.329 2.848 -1.519 1.40e-02 5.10e+03 1.18e+04 bond pdb=" N TRP B 459 " pdb=" CA TRP B 459 " ideal model delta sigma weight residual 1.463 1.382 0.081 1.31e-02 5.83e+03 3.81e+01 bond pdb=" CA PRO R 433 " pdb=" C PRO R 433 " ideal model delta sigma weight residual 1.517 1.574 -0.057 9.30e-03 1.16e+04 3.80e+01 bond pdb=" N VAL R 430 " pdb=" CA VAL R 430 " ideal model delta sigma weight residual 1.456 1.511 -0.055 1.11e-02 8.12e+03 2.49e+01 bond pdb=" CB SER N 28 " pdb=" OG SER N 28 " ideal model delta sigma weight residual 1.417 1.505 -0.088 2.00e-02 2.50e+03 1.92e+01 ... (remaining 38799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.61: 52388 5.61 - 11.21: 130 11.21 - 16.82: 17 16.82 - 22.42: 3 22.42 - 28.03: 1 Bond angle restraints: 52539 Sorted by residual: angle pdb=" N VAL R 431 " pdb=" CA VAL R 431 " pdb=" C VAL R 431 " ideal model delta sigma weight residual 110.74 138.77 -28.03 9.10e-01 1.21e+00 9.49e+02 angle pdb=" N VAL C 15 " pdb=" CA VAL C 15 " pdb=" C VAL C 15 " ideal model delta sigma weight residual 109.30 91.47 17.83 1.25e+00 6.40e-01 2.04e+02 angle pdb=" N TYR B 17 " pdb=" CA TYR B 17 " pdb=" C TYR B 17 " ideal model delta sigma weight residual 112.89 99.06 13.83 1.24e+00 6.50e-01 1.24e+02 angle pdb=" O ASP R 367 " pdb=" C ASP R 367 " pdb=" N ARG R 369 " ideal model delta sigma weight residual 121.74 107.25 14.49 1.31e+00 5.83e-01 1.22e+02 angle pdb=" N PRO R 433 " pdb=" CA PRO R 433 " pdb=" C PRO R 433 " ideal model delta sigma weight residual 110.70 123.72 -13.02 1.22e+00 6.72e-01 1.14e+02 ... (remaining 52534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 20239 17.98 - 35.96: 2005 35.96 - 53.94: 464 53.94 - 71.92: 125 71.92 - 89.90: 44 Dihedral angle restraints: 22877 sinusoidal: 9100 harmonic: 13777 Sorted by residual: dihedral pdb=" N ALA R 301 " pdb=" C ALA R 301 " pdb=" CA ALA R 301 " pdb=" CB ALA R 301 " ideal model delta harmonic sigma weight residual 122.90 154.13 -31.23 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" C ALA R 301 " pdb=" N ALA R 301 " pdb=" CA ALA R 301 " pdb=" CB ALA R 301 " ideal model delta harmonic sigma weight residual -122.60 -153.73 31.13 0 2.50e+00 1.60e-01 1.55e+02 dihedral pdb=" CB CYS O 19 " pdb=" SG CYS O 19 " pdb=" SG CYS O 65 " pdb=" CB CYS O 65 " ideal model delta sinusoidal sigma weight residual -86.00 -175.75 89.75 1 1.00e+01 1.00e-02 9.56e+01 ... (remaining 22874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.281: 5615 0.281 - 0.561: 22 0.561 - 0.842: 4 0.842 - 1.122: 0 1.122 - 1.403: 1 Chirality restraints: 5642 Sorted by residual: chirality pdb=" CA ALA R 301 " pdb=" N ALA R 301 " pdb=" C ALA R 301 " pdb=" CB ALA R 301 " both_signs ideal model delta sigma weight residual False 2.48 1.08 1.40 2.00e-01 2.50e+01 4.92e+01 chirality pdb=" CA LYS Q 10 " pdb=" N LYS Q 10 " pdb=" C LYS Q 10 " pdb=" CB LYS Q 10 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CA LYS N 10 " pdb=" N LYS N 10 " pdb=" C LYS N 10 " pdb=" CB LYS N 10 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.75e+01 ... (remaining 5639 not shown) Planarity restraints: 6889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP R 367 " -0.116 2.00e-02 2.50e+03 1.80e-01 3.25e+02 pdb=" C ASP R 367 " 0.306 2.00e-02 2.50e+03 pdb=" O ASP R 367 " -0.144 2.00e-02 2.50e+03 pdb=" N ARG R 369 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 169 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C CYS B 169 " -0.067 2.00e-02 2.50e+03 pdb=" O CYS B 169 " 0.025 2.00e-02 2.50e+03 pdb=" N THR B 170 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE S 326 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE S 326 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE S 326 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE S 327 " 0.019 2.00e-02 2.50e+03 ... (remaining 6886 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 11 2.16 - 2.85: 13278 2.85 - 3.53: 48190 3.53 - 4.22: 86022 4.22 - 4.90: 157363 Nonbonded interactions: 304864 Sorted by model distance: nonbonded pdb=" NZ LYS B 172 " pdb=" N GLY B 401 " model vdw 1.476 3.200 nonbonded pdb=" NZ LYS B 460 " pdb=" OD1 ASP Q 64 " model vdw 1.655 3.120 nonbonded pdb=" CZ3 TRP J 459 " pdb=" OD1 ASN N 66 " model vdw 1.790 3.340 nonbonded pdb=" CE LYS B 172 " pdb=" N GLY B 401 " model vdw 1.856 3.520 nonbonded pdb=" NZ LYS B 172 " pdb=" CA GLY B 401 " model vdw 1.914 3.520 ... (remaining 304859 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 466) selection = chain 'B' selection = (chain 'F' and resid 14 through 466) selection = (chain 'G' and resid 14 through 466) selection = (chain 'H' and resid 14 through 466) selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'C' and resid 7 through 77) selection = (chain 'L' and resid 7 through 77) selection = (chain 'M' and resid 7 through 77) selection = (chain 'N' and resid 7 through 77) selection = (chain 'O' and resid 7 through 77) selection = (chain 'P' and resid 7 through 77) selection = (chain 'Q' and resid 7 through 77) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = (chain 'R' and (resid 288 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB )) or resid 295 through 357 or (resid 358 and (name N \ or name CA or name C or name O or name CB )) or resid 359 through 369 or (resid \ 370 and (name N or name CA or name C or name O or name CB )) or resid 371 throug \ h 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) or \ resid 409 through 418 or (resid 419 and (name N or name CA or name C or name O o \ r name CB )) or resid 420 through 435 or (resid 436 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'S' and (resid 288 through 316 or (resid 317 and (name N or name CA or na \ me C or name O or name CB )) or resid 318 through 367 or (resid 369 through 370 \ and (name N or name CA or name C or name O or name CB )) or resid 371 through 43 \ 6)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 37.310 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 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 : 0.013 1.519 38813 Z= 0.718 Angle : 0.991 28.031 52555 Z= 0.603 Chirality : 0.070 1.403 5642 Planarity : 0.006 0.180 6889 Dihedral : 15.765 89.895 14069 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.77 % Favored : 91.00 % Rotamer: Outliers : 4.66 % Allowed : 7.16 % Favored : 88.18 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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 aren not related in a simple way. whole: -3.01 (0.10), residues: 4846 helix: -1.15 (0.11), residues: 1715 sheet: -0.88 (0.22), residues: 455 loop : -2.90 (0.10), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 131 TYR 0.012 0.002 TYR E 167 PHE 0.029 0.002 PHE G 342 TRP 0.037 0.002 TRP G 408 HIS 0.007 0.002 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.01262 (38804) covalent geometry : angle 0.99030 (52539) SS BOND : bond 0.09362 ( 8) SS BOND : angle 2.19333 ( 16) hydrogen bonds : bond 0.15802 ( 1425) hydrogen bonds : angle 6.14076 ( 4080) Misc. bond : bond 0.07040 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9692 Ramachandran restraints generated. 4846 Oldfield, 0 Emsley, 4846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 856 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 THR cc_start: 0.7485 (p) cc_final: 0.7282 (t) REVERT: A 174 LYS cc_start: 0.4779 (mppt) cc_final: 0.4550 (mttt) REVERT: A 393 ASP cc_start: 0.8155 (p0) cc_final: 0.7525 (m-30) REVERT: A 457 ASP cc_start: 0.5845 (m-30) cc_final: 0.5604 (m-30) REVERT: B 17 TYR cc_start: 0.3165 (OUTLIER) cc_final: 0.2875 (p90) REVERT: B 25 ASP cc_start: 0.7181 (p0) cc_final: 0.6949 (p0) REVERT: B 249 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7789 (mtmt) REVERT: B 336 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6771 (tmmt) REVERT: B 389 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: B 437 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.5268 (pt0) REVERT: C 16 CYS cc_start: 0.6480 (OUTLIER) cc_final: 0.5402 (p) REVERT: C 58 LYS cc_start: 0.7678 (mttt) cc_final: 0.6767 (tptt) REVERT: C 66 ASN cc_start: 0.5965 (m-40) cc_final: 0.5354 (t0) REVERT: C 71 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6552 (mm) REVERT: D 9 ARG cc_start: 0.6368 (tpp-160) cc_final: 0.5524 (mmm-85) REVERT: D 19 PHE cc_start: 0.5852 (m-80) cc_final: 0.5551 (m-80) REVERT: D 35 MET cc_start: 0.7303 (mtm) cc_final: 0.6700 (mmm) REVERT: D 59 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6638 (tm-30) REVERT: D 202 THR cc_start: 0.7264 (m) cc_final: 0.6938 (p) REVERT: E 1 MET cc_start: 0.1775 (ttp) cc_final: 0.0924 (ppp) REVERT: E 132 GLN cc_start: 0.5804 (mt0) cc_final: 0.5304 (mt0) REVERT: F 25 ASP cc_start: 0.6666 (p0) cc_final: 0.6087 (m-30) REVERT: F 77 TYR cc_start: 0.8195 (m-80) cc_final: 0.7758 (m-80) REVERT: F 125 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7653 (ttmt) REVERT: F 222 ILE cc_start: 0.8855 (mt) cc_final: 0.8492 (mt) REVERT: F 315 LEU cc_start: 0.8503 (tp) cc_final: 0.8289 (tp) REVERT: F 426 GLN cc_start: 0.7434 (tp40) cc_final: 0.7124 (tp-100) REVERT: F 469 MET cc_start: 0.2807 (mmt) cc_final: 0.2407 (mpp) REVERT: G 73 ASP cc_start: 0.3560 (OUTLIER) cc_final: 0.3164 (p0) REVERT: G 109 SER cc_start: 0.8754 (t) cc_final: 0.8491 (p) REVERT: G 125 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7545 (mttp) REVERT: G 128 ARG cc_start: 0.7536 (ttp80) cc_final: 0.7165 (ttp-170) REVERT: G 191 ARG cc_start: 0.7683 (tpt90) cc_final: 0.7470 (tpt90) REVERT: G 444 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6910 (tm-30) REVERT: H 80 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7813 (mptt) REVERT: H 92 ASN cc_start: 0.7601 (t0) cc_final: 0.7104 (t0) REVERT: H 125 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7771 (mttt) REVERT: H 301 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7427 (mt0) REVERT: I 23 THR cc_start: 0.8015 (p) cc_final: 0.7803 (t) REVERT: I 76 ARG cc_start: 0.6909 (ptm-80) cc_final: 0.6689 (ptt90) REVERT: I 94 TYR cc_start: 0.8268 (m-80) cc_final: 0.7881 (m-80) REVERT: I 118 VAL cc_start: 0.8464 (t) cc_final: 0.8242 (m) REVERT: I 169 CYS cc_start: 0.8152 (p) cc_final: 0.7929 (t) REVERT: I 340 LEU cc_start: 0.7568 (mt) cc_final: 0.7281 (mt) REVERT: I 384 MET cc_start: 0.7757 (tpp) cc_final: 0.7552 (tpp) REVERT: I 426 GLN cc_start: 0.7387 (tp40) cc_final: 0.7019 (pt0) REVERT: I 448 TRP cc_start: 0.6212 (p-90) cc_final: 0.5513 (p90) REVERT: I 460 LYS cc_start: 0.7901 (mtpt) cc_final: 0.7393 (mmtt) REVERT: J 74 MET cc_start: 0.6735 (tmm) cc_final: 0.6125 (ptt) REVERT: J 175 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6296 (mt) REVERT: J 200 ASP cc_start: 0.6551 (t0) cc_final: 0.6211 (t70) REVERT: K 32 ASP cc_start: 0.7158 (m-30) cc_final: 0.6924 (m-30) REVERT: K 74 MET cc_start: 0.3513 (tpt) cc_final: 0.3176 (mtp) REVERT: K 231 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6841 (tt0) REVERT: K 299 ASP cc_start: 0.7004 (p0) cc_final: 0.6696 (p0) REVERT: K 422 GLU cc_start: 0.6556 (mt-10) cc_final: 0.6317 (mm-30) REVERT: L 58 LYS cc_start: 0.7850 (mttp) cc_final: 0.7644 (mtmt) REVERT: M 22 GLU cc_start: 0.7017 (tt0) cc_final: 0.6254 (tp30) REVERT: M 53 LEU cc_start: 0.8281 (tp) cc_final: 0.8028 (tp) REVERT: M 57 LYS cc_start: 0.7581 (mmmm) cc_final: 0.7124 (mmmm) REVERT: O 18 ASN cc_start: 0.7383 (t0) cc_final: 0.7167 (t0) REVERT: Q 12 ASN cc_start: 0.6242 (OUTLIER) cc_final: 0.5870 (p0) REVERT: R 342 LYS cc_start: 0.0550 (OUTLIER) cc_final: -0.0122 (mmtm) REVERT: R 346 VAL cc_start: 0.2693 (m) cc_final: 0.2057 (m) REVERT: R 347 LEU cc_start: 0.3705 (OUTLIER) cc_final: 0.3431 (mm) REVERT: R 431 VAL cc_start: 0.2214 (OUTLIER) cc_final: 0.1748 (p) REVERT: S 336 GLU cc_start: 0.1890 (OUTLIER) cc_final: 0.1207 (tt0) REVERT: S 347 LEU cc_start: -0.0053 (OUTLIER) cc_final: -0.0387 (tt) REVERT: S 363 VAL cc_start: 0.0223 (OUTLIER) cc_final: -0.0217 (t) REVERT: S 369 ARG cc_start: 0.1852 (OUTLIER) cc_final: 0.1231 (ppt170) REVERT: S 393 GLU cc_start: 0.0519 (OUTLIER) cc_final: 0.0157 (pp20) outliers start: 184 outliers final: 35 residues processed: 1007 average time/residue: 0.2715 time to fit residues: 424.5575 Evaluate side-chains 589 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 537 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 62 CYS Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 288 ILE Chi-restraints excluded: chain R residue 303 SER Chi-restraints excluded: chain R residue 313 GLU Chi-restraints excluded: chain R residue 316 GLU Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 366 ARG Chi-restraints excluded: chain R residue 370 LYS Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 379 GLU Chi-restraints excluded: chain R residue 405 ASN Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 413 SER Chi-restraints excluded: chain R residue 418 ARG Chi-restraints excluded: chain R residue 431 VAL Chi-restraints excluded: chain R residue 435 ARG Chi-restraints excluded: chain S residue 288 ILE Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 335 VAL Chi-restraints excluded: chain S residue 336 GLU Chi-restraints excluded: chain S residue 343 ARG Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 369 ARG Chi-restraints excluded: chain S residue 389 ARG Chi-restraints excluded: chain S residue 393 GLU Chi-restraints excluded: chain S residue 401 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.6980 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 470 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 92 ASN A 112 ASN A 160 ASN A 209 GLN A 322 HIS A 383 HIS A 417 ASN A 429 ASN B 146 GLN C 7 GLN D 6 GLN D 77 GLN D 84 GLN E 70 ASN E 84 GLN F 202 ASN F 417 ASN G 112 ASN G 181 ASN G 209 GLN G 301 GLN G 322 HIS G 350 HIS ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 417 ASN G 426 GLN H 112 ASN H 181 ASN H 307 HIS J 92 ASN ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 291 HIS K 146 GLN L 29 GLN M 12 ASN M 18 ASN M 66 ASN P 5 ASN P 12 ASN P 44 GLN Q 36 ASN Q 66 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.172771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139730 restraints weight = 45547.116| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.61 r_work: 0.3201 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38813 Z= 0.138 Angle : 0.641 15.511 52555 Z= 0.337 Chirality : 0.045 0.243 5642 Planarity : 0.005 0.108 6889 Dihedral : 7.043 84.875 5389 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.20 % Rotamer: Outliers : 2.88 % Allowed : 12.22 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.80 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.36 (0.12), residues: 4848 helix: 0.55 (0.13), residues: 1740 sheet: -0.52 (0.20), residues: 512 loop : -2.10 (0.11), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 191 TYR 0.021 0.001 TYR E 41 PHE 0.039 0.002 PHE S 332 TRP 0.017 0.001 TRP G 408 HIS 0.009 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00305 (38804) covalent geometry : angle 0.64095 (52539) SS BOND : bond 0.01357 ( 8) SS BOND : angle 1.20658 ( 16) hydrogen bonds : bond 0.04181 ( 1425) hydrogen bonds : angle 4.28213 ( 4080) Misc. bond : bond 0.01086 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 593 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7590 (tp30) REVERT: A 174 LYS cc_start: 0.5432 (mppt) cc_final: 0.4871 (mttm) REVERT: A 302 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7967 (ttt180) REVERT: A 393 ASP cc_start: 0.8604 (p0) cc_final: 0.7904 (m-30) REVERT: A 456 LEU cc_start: 0.8255 (mt) cc_final: 0.7983 (mt) REVERT: B 17 TYR cc_start: 0.3295 (OUTLIER) cc_final: 0.3017 (p90) REVERT: B 25 ASP cc_start: 0.7137 (p0) cc_final: 0.6800 (p0) REVERT: B 57 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7355 (tt0) REVERT: B 74 MET cc_start: 0.5603 (tpp) cc_final: 0.4688 (mmt) REVERT: B 245 GLU cc_start: 0.7524 (mp0) cc_final: 0.7295 (mp0) REVERT: B 302 ARG cc_start: 0.8388 (tmm-80) cc_final: 0.7967 (ttt-90) REVERT: B 389 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: C 18 ASN cc_start: 0.6499 (t0) cc_final: 0.6245 (t0) REVERT: C 22 GLU cc_start: 0.5904 (tt0) cc_final: 0.5621 (tp30) REVERT: C 58 LYS cc_start: 0.7874 (mttt) cc_final: 0.6667 (tptt) REVERT: C 66 ASN cc_start: 0.7288 (m-40) cc_final: 0.6732 (t0) REVERT: C 74 PHE cc_start: 0.2153 (OUTLIER) cc_final: 0.1283 (m-80) REVERT: D 19 PHE cc_start: 0.6964 (m-80) cc_final: 0.6641 (m-80) REVERT: D 96 ASP cc_start: 0.7101 (t0) cc_final: 0.6529 (p0) REVERT: D 178 ASP cc_start: 0.6673 (t70) cc_final: 0.6379 (t0) REVERT: E 1 MET cc_start: 0.1771 (ttp) cc_final: 0.1001 (ppp) REVERT: E 35 MET cc_start: 0.5504 (tmm) cc_final: 0.5243 (ptp) REVERT: E 83 LEU cc_start: 0.5351 (OUTLIER) cc_final: 0.4940 (mp) REVERT: E 132 GLN cc_start: 0.6870 (mt0) cc_final: 0.6425 (mt0) REVERT: E 136 ARG cc_start: 0.6127 (ttm110) cc_final: 0.5255 (mmt180) REVERT: F 23 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7833 (p) REVERT: F 25 ASP cc_start: 0.7323 (p0) cc_final: 0.6556 (m-30) REVERT: F 125 LYS cc_start: 0.8322 (mmmt) cc_final: 0.7971 (ttmt) REVERT: F 222 ILE cc_start: 0.9146 (mt) cc_final: 0.8727 (mm) REVERT: F 247 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8574 (ttp) REVERT: F 426 GLN cc_start: 0.7862 (tp40) cc_final: 0.7577 (tp-100) REVERT: F 469 MET cc_start: 0.2733 (mmt) cc_final: 0.2265 (mpp) REVERT: G 73 ASP cc_start: 0.2637 (OUTLIER) cc_final: 0.2082 (p0) REVERT: G 109 SER cc_start: 0.8683 (t) cc_final: 0.8431 (p) REVERT: G 128 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7939 (ttp-170) REVERT: G 166 MET cc_start: 0.8408 (mtm) cc_final: 0.8167 (mtt) REVERT: G 346 MET cc_start: 0.8780 (ptt) cc_final: 0.8499 (ptt) REVERT: G 349 ASP cc_start: 0.6866 (t70) cc_final: 0.6657 (t0) REVERT: G 426 GLN cc_start: 0.7505 (tp40) cc_final: 0.7117 (tp-100) REVERT: G 432 ARG cc_start: 0.7407 (mtm180) cc_final: 0.6789 (ttt180) REVERT: H 74 MET cc_start: 0.6261 (ptm) cc_final: 0.6050 (ptm) REVERT: H 76 ARG cc_start: 0.7679 (mtm180) cc_final: 0.7420 (mtm180) REVERT: H 92 ASN cc_start: 0.7539 (t0) cc_final: 0.7204 (t0) REVERT: H 469 MET cc_start: 0.3850 (ttm) cc_final: 0.3468 (tpp) REVERT: I 74 MET cc_start: 0.6032 (ptm) cc_final: 0.5517 (ptm) REVERT: I 248 MET cc_start: 0.8842 (mmt) cc_final: 0.8570 (mmp) REVERT: I 267 LEU cc_start: 0.8532 (mt) cc_final: 0.8258 (mt) REVERT: I 426 GLN cc_start: 0.8020 (tp40) cc_final: 0.7412 (pt0) REVERT: I 448 TRP cc_start: 0.6449 (p-90) cc_final: 0.5687 (p90) REVERT: I 460 LYS cc_start: 0.8304 (mtpt) cc_final: 0.7757 (mmtt) REVERT: J 74 MET cc_start: 0.6861 (tmm) cc_final: 0.6324 (ptt) REVERT: J 175 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6214 (mt) REVERT: J 436 ARG cc_start: 0.6585 (tpp80) cc_final: 0.6378 (ttm-80) REVERT: K 32 ASP cc_start: 0.7763 (m-30) cc_final: 0.7518 (m-30) REVERT: K 228 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6834 (tm-30) REVERT: K 348 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7339 (mt-10) REVERT: K 422 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7288 (mm-30) REVERT: K 435 TYR cc_start: 0.7603 (m-10) cc_final: 0.7372 (m-80) REVERT: L 58 LYS cc_start: 0.8099 (mttp) cc_final: 0.7893 (mtmt) REVERT: M 22 GLU cc_start: 0.7648 (tt0) cc_final: 0.7001 (tp30) REVERT: M 38 ILE cc_start: 0.5565 (OUTLIER) cc_final: 0.5257 (pt) REVERT: M 57 LYS cc_start: 0.7877 (mmmm) cc_final: 0.7624 (mmmm) REVERT: O 18 ASN cc_start: 0.7403 (t0) cc_final: 0.7187 (t0) REVERT: P 5 ASN cc_start: 0.3412 (OUTLIER) cc_final: 0.3171 (m110) REVERT: Q 12 ASN cc_start: 0.7266 (OUTLIER) cc_final: 0.6296 (p0) REVERT: R 342 LYS cc_start: -0.0044 (OUTLIER) cc_final: -0.0298 (mmtp) REVERT: S 393 GLU cc_start: 0.0532 (OUTLIER) cc_final: 0.0258 (pp20) REVERT: S 426 MET cc_start: 0.1106 (ptm) cc_final: 0.0461 (ttp) outliers start: 114 outliers final: 52 residues processed: 684 average time/residue: 0.2549 time to fit residues: 274.6152 Evaluate side-chains 562 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 497 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 247 MET Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 189 CYS Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 5 ASN Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 370 LYS Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 379 GLU Chi-restraints excluded: chain R residue 405 ASN Chi-restraints excluded: chain R residue 418 ARG Chi-restraints excluded: chain S residue 303 SER Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 335 VAL Chi-restraints excluded: chain S residue 369 ARG Chi-restraints excluded: chain S residue 393 GLU Chi-restraints excluded: chain S residue 401 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 263 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 326 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 456 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 435 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 304 HIS D 70 ASN E 6 GLN E 84 GLN E 113 GLN F 289 HIS G 209 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 GLN H 209 GLN H 350 HIS H 417 ASN I 209 GLN ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN ** P 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.168415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134543 restraints weight = 45930.220| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.78 r_work: 0.3156 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 38813 Z= 0.225 Angle : 0.704 11.069 52555 Z= 0.366 Chirality : 0.049 0.278 5642 Planarity : 0.006 0.110 6889 Dihedral : 6.381 87.413 5323 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.16 % Favored : 92.76 % Rotamer: Outliers : 3.59 % Allowed : 14.47 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.80 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.96 (0.12), residues: 4848 helix: 0.89 (0.13), residues: 1739 sheet: -0.41 (0.20), residues: 552 loop : -1.86 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 191 TYR 0.024 0.002 TYR E 5 PHE 0.031 0.002 PHE K 342 TRP 0.025 0.002 TRP G 408 HIS 0.010 0.002 HIS J 150 Details of bonding type rmsd covalent geometry : bond 0.00544 (38804) covalent geometry : angle 0.70357 (52539) SS BOND : bond 0.01602 ( 8) SS BOND : angle 1.25565 ( 16) hydrogen bonds : bond 0.05753 ( 1425) hydrogen bonds : angle 4.25379 ( 4080) Misc. bond : bond 0.00108 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 522 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.5222 (mppt) cc_final: 0.4731 (mtpt) REVERT: B 25 ASP cc_start: 0.7036 (p0) cc_final: 0.6755 (p0) REVERT: B 302 ARG cc_start: 0.8220 (tmm-80) cc_final: 0.7886 (ttt-90) REVERT: B 389 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: C 22 GLU cc_start: 0.6479 (tt0) cc_final: 0.6201 (tp30) REVERT: C 38 ILE cc_start: -0.1463 (OUTLIER) cc_final: -0.2142 (tp) REVERT: C 58 LYS cc_start: 0.7924 (mttt) cc_final: 0.6878 (tptt) REVERT: C 66 ASN cc_start: 0.8093 (m-40) cc_final: 0.7642 (t0) REVERT: C 70 PHE cc_start: 0.8775 (p90) cc_final: 0.8505 (p90) REVERT: C 74 PHE cc_start: 0.2268 (OUTLIER) cc_final: 0.0874 (m-10) REVERT: D 96 ASP cc_start: 0.7306 (t0) cc_final: 0.6649 (p0) REVERT: D 139 LYS cc_start: 0.8442 (mmtm) cc_final: 0.7973 (mmtp) REVERT: D 178 ASP cc_start: 0.6772 (t70) cc_final: 0.6429 (t0) REVERT: E 1 MET cc_start: 0.2677 (ttp) cc_final: 0.2090 (ptm) REVERT: E 35 MET cc_start: 0.5382 (tmm) cc_final: 0.5086 (ptp) REVERT: E 132 GLN cc_start: 0.7060 (mt0) cc_final: 0.6318 (mt0) REVERT: E 136 ARG cc_start: 0.6317 (ttm110) cc_final: 0.5290 (mmt180) REVERT: F 23 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7821 (p) REVERT: F 25 ASP cc_start: 0.6971 (p0) cc_final: 0.6343 (m-30) REVERT: F 125 LYS cc_start: 0.8344 (mmmt) cc_final: 0.7989 (ttmt) REVERT: F 222 ILE cc_start: 0.9137 (mt) cc_final: 0.8791 (mt) REVERT: F 384 MET cc_start: 0.7602 (tpp) cc_final: 0.7256 (mmm) REVERT: F 426 GLN cc_start: 0.7898 (tp40) cc_final: 0.7532 (tp-100) REVERT: F 469 MET cc_start: 0.3033 (mmt) cc_final: 0.2454 (mpp) REVERT: G 73 ASP cc_start: 0.2997 (OUTLIER) cc_final: 0.2546 (p0) REVERT: G 98 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8443 (pt) REVERT: G 109 SER cc_start: 0.8672 (t) cc_final: 0.8452 (p) REVERT: G 128 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7734 (ttp-170) REVERT: G 166 MET cc_start: 0.8212 (mtm) cc_final: 0.7895 (mtt) REVERT: G 349 ASP cc_start: 0.6946 (t70) cc_final: 0.6539 (t0) REVERT: G 426 GLN cc_start: 0.7524 (tp40) cc_final: 0.7009 (tp-100) REVERT: G 428 ARG cc_start: 0.7350 (ttp-170) cc_final: 0.7123 (ttp80) REVERT: G 444 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6914 (tm-30) REVERT: H 57 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7552 (mm-30) REVERT: H 92 ASN cc_start: 0.7800 (t0) cc_final: 0.7415 (t0) REVERT: H 283 ASP cc_start: 0.7310 (m-30) cc_final: 0.6868 (m-30) REVERT: H 469 MET cc_start: 0.3690 (ttm) cc_final: 0.3262 (tpp) REVERT: I 267 LEU cc_start: 0.8586 (mt) cc_final: 0.8356 (mt) REVERT: I 426 GLN cc_start: 0.7969 (tp40) cc_final: 0.7416 (pt0) REVERT: I 460 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7652 (mmtt) REVERT: J 23 THR cc_start: 0.7640 (m) cc_final: 0.7214 (p) REVERT: J 49 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: J 357 ARG cc_start: 0.7748 (mtp85) cc_final: 0.7376 (mtm180) REVERT: K 279 LYS cc_start: 0.8749 (mttt) cc_final: 0.8471 (mmtp) REVERT: L 50 LEU cc_start: 0.7527 (mp) cc_final: 0.7265 (mt) REVERT: M 57 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7922 (mmmm) REVERT: O 22 GLU cc_start: 0.6984 (mp0) cc_final: 0.6751 (mm-30) REVERT: R 324 MET cc_start: -0.0297 (mmm) cc_final: -0.1474 (ptm) REVERT: R 342 LYS cc_start: 0.0228 (OUTLIER) cc_final: -0.0207 (mmtt) REVERT: S 393 GLU cc_start: 0.0658 (OUTLIER) cc_final: 0.0161 (pp20) REVERT: S 426 MET cc_start: 0.0785 (ptm) cc_final: 0.0058 (ttp) outliers start: 142 outliers final: 88 residues processed: 631 average time/residue: 0.2733 time to fit residues: 273.3339 Evaluate side-chains 570 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 473 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 189 CYS Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 424 CYS Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 209 GLN Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 424 CYS Chi-restraints excluded: chain H residue 425 VAL Chi-restraints excluded: chain H residue 460 LYS Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 189 CYS Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 376 SER Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 62 CYS Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 370 LYS Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 405 ASN Chi-restraints excluded: chain R residue 418 ARG Chi-restraints excluded: chain R residue 431 VAL Chi-restraints excluded: chain S residue 303 SER Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 335 VAL Chi-restraints excluded: chain S residue 369 ARG Chi-restraints excluded: chain S residue 393 GLU Chi-restraints excluded: chain S residue 401 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 334 optimal weight: 2.9990 chunk 387 optimal weight: 4.9990 chunk 368 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 312 optimal weight: 0.9990 chunk 154 optimal weight: 0.1980 chunk 379 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 304 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN E 84 GLN E 113 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 383 HIS I 209 GLN ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.168743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134786 restraints weight = 45561.115| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.84 r_work: 0.3111 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 38813 Z= 0.150 Angle : 0.612 10.466 52555 Z= 0.318 Chirality : 0.045 0.219 5642 Planarity : 0.005 0.077 6889 Dihedral : 5.969 85.466 5314 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.25 % Favored : 93.67 % Rotamer: Outliers : 3.09 % Allowed : 16.45 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.80 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.59 (0.12), residues: 4848 helix: 1.31 (0.13), residues: 1732 sheet: -0.27 (0.20), residues: 571 loop : -1.71 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG A 191 TYR 0.017 0.001 TYR D 41 PHE 0.022 0.002 PHE B 342 TRP 0.020 0.001 TRP G 408 HIS 0.007 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00352 (38804) covalent geometry : angle 0.61144 (52539) SS BOND : bond 0.01338 ( 8) SS BOND : angle 0.96356 ( 16) hydrogen bonds : bond 0.04383 ( 1425) hydrogen bonds : angle 4.04301 ( 4080) Misc. bond : bond 0.00125 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 502 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.5391 (mppt) cc_final: 0.4635 (mttm) REVERT: A 226 GLN cc_start: 0.8512 (tt0) cc_final: 0.8279 (tt0) REVERT: A 444 GLU cc_start: 0.7807 (pp20) cc_final: 0.6929 (mp0) REVERT: B 74 MET cc_start: 0.5238 (tpp) cc_final: 0.4324 (mmt) REVERT: B 389 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: C 58 LYS cc_start: 0.8079 (mttt) cc_final: 0.6967 (tptt) REVERT: C 66 ASN cc_start: 0.8171 (m-40) cc_final: 0.7783 (t0) REVERT: C 70 PHE cc_start: 0.8838 (p90) cc_final: 0.8418 (p90) REVERT: C 74 PHE cc_start: 0.2080 (OUTLIER) cc_final: 0.0888 (m-10) REVERT: D 139 LYS cc_start: 0.8526 (mmtm) cc_final: 0.8052 (mmtp) REVERT: D 178 ASP cc_start: 0.6656 (t70) cc_final: 0.6319 (t0) REVERT: E 1 MET cc_start: 0.2672 (ttp) cc_final: 0.2020 (ptm) REVERT: E 34 ARG cc_start: 0.5221 (mmt-90) cc_final: 0.4876 (mmt180) REVERT: E 35 MET cc_start: 0.5376 (tmm) cc_final: 0.4971 (ptp) REVERT: E 83 LEU cc_start: 0.5094 (OUTLIER) cc_final: 0.4762 (mp) REVERT: E 132 GLN cc_start: 0.6887 (mt0) cc_final: 0.6146 (mt0) REVERT: E 136 ARG cc_start: 0.6325 (ttm110) cc_final: 0.5293 (mmt180) REVERT: F 23 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7809 (p) REVERT: F 25 ASP cc_start: 0.7229 (p0) cc_final: 0.6433 (m-30) REVERT: F 125 LYS cc_start: 0.8474 (mmmt) cc_final: 0.7954 (ttmt) REVERT: F 222 ILE cc_start: 0.9147 (mt) cc_final: 0.8852 (mt) REVERT: F 384 MET cc_start: 0.7752 (tpp) cc_final: 0.7451 (mmm) REVERT: F 426 GLN cc_start: 0.7901 (tp40) cc_final: 0.7627 (tp-100) REVERT: F 469 MET cc_start: 0.2893 (mmt) cc_final: 0.2163 (mpp) REVERT: G 73 ASP cc_start: 0.2853 (OUTLIER) cc_final: 0.2499 (p0) REVERT: G 109 SER cc_start: 0.8735 (t) cc_final: 0.8523 (p) REVERT: G 128 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7872 (ttp-170) REVERT: G 166 MET cc_start: 0.8396 (mtm) cc_final: 0.8053 (mtt) REVERT: G 349 ASP cc_start: 0.7181 (t70) cc_final: 0.6707 (t0) REVERT: G 426 GLN cc_start: 0.7592 (tp40) cc_final: 0.7185 (tp40) REVERT: G 444 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6917 (tm-30) REVERT: H 57 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7869 (mm-30) REVERT: H 92 ASN cc_start: 0.7919 (t0) cc_final: 0.7318 (t0) REVERT: H 283 ASP cc_start: 0.7584 (m-30) cc_final: 0.7123 (m-30) REVERT: H 469 MET cc_start: 0.3564 (ttm) cc_final: 0.3224 (tpp) REVERT: I 166 MET cc_start: 0.9028 (mtm) cc_final: 0.8570 (mpp) REVERT: I 267 LEU cc_start: 0.8606 (mt) cc_final: 0.8360 (mt) REVERT: I 426 GLN cc_start: 0.8049 (tp40) cc_final: 0.7360 (pt0) REVERT: I 460 LYS cc_start: 0.8173 (mtpt) cc_final: 0.7622 (mmtt) REVERT: J 23 THR cc_start: 0.7617 (m) cc_final: 0.7115 (p) REVERT: J 357 ARG cc_start: 0.7781 (mtp85) cc_final: 0.7383 (mtm180) REVERT: J 436 ARG cc_start: 0.7009 (tpp80) cc_final: 0.6478 (mtp85) REVERT: K 203 ILE cc_start: 0.8474 (mt) cc_final: 0.8245 (pt) REVERT: K 279 LYS cc_start: 0.8838 (mttt) cc_final: 0.8595 (mmtp) REVERT: L 10 LYS cc_start: 0.5985 (mtmt) cc_final: 0.5678 (mtmt) REVERT: L 50 LEU cc_start: 0.7526 (mp) cc_final: 0.7311 (mt) REVERT: M 57 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7900 (mmmt) REVERT: N 36 ASN cc_start: 0.6860 (t0) cc_final: 0.6375 (t0) REVERT: N 57 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6548 (mmtm) REVERT: N 70 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: O 22 GLU cc_start: 0.7016 (mp0) cc_final: 0.6810 (mm-30) REVERT: R 324 MET cc_start: 0.0164 (mmm) cc_final: -0.1342 (ptm) REVERT: R 342 LYS cc_start: 0.0269 (OUTLIER) cc_final: -0.0144 (mmtt) REVERT: S 393 GLU cc_start: 0.0733 (OUTLIER) cc_final: 0.0498 (pp20) outliers start: 122 outliers final: 79 residues processed: 594 average time/residue: 0.2585 time to fit residues: 244.2892 Evaluate side-chains 555 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 467 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 433 ASP Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 155 GLU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 460 LYS Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 189 CYS Chi-restraints excluded: chain I residue 249 LYS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 424 CYS Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 62 CYS Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 431 VAL Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 327 ILE Chi-restraints excluded: chain S residue 335 VAL Chi-restraints excluded: chain S residue 393 GLU Chi-restraints excluded: chain S residue 401 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 247 optimal weight: 0.8980 chunk 224 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 420 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 chunk 212 optimal weight: 5.9990 chunk 255 optimal weight: 0.1980 chunk 173 optimal weight: 6.9990 chunk 445 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 442 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 146 GLN E 84 GLN E 113 GLN F 417 ASN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN I 209 GLN ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 12 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 12 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.169730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.136002 restraints weight = 45813.455| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.89 r_work: 0.3207 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 38813 Z= 0.106 Angle : 0.555 10.697 52555 Z= 0.286 Chirality : 0.043 0.279 5642 Planarity : 0.005 0.209 6889 Dihedral : 5.355 81.230 5300 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.08 % Favored : 93.85 % Rotamer: Outliers : 2.56 % Allowed : 17.74 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.80 % 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 aren not related in a simple way. whole: -0.16 (0.12), residues: 4848 helix: 1.76 (0.13), residues: 1740 sheet: -0.23 (0.20), residues: 595 loop : -1.50 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG A 191 TYR 0.018 0.001 TYR D 41 PHE 0.018 0.001 PHE H 466 TRP 0.015 0.001 TRP H 408 HIS 0.007 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00234 (38804) covalent geometry : angle 0.55469 (52539) SS BOND : bond 0.01086 ( 8) SS BOND : angle 0.72804 ( 16) hydrogen bonds : bond 0.03355 ( 1425) hydrogen bonds : angle 3.81278 ( 4080) Misc. bond : bond 0.00328 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 513 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.5524 (mppt) cc_final: 0.4689 (mttm) REVERT: A 226 GLN cc_start: 0.8454 (tt0) cc_final: 0.8197 (tt0) REVERT: A 294 MET cc_start: 0.8918 (ttp) cc_final: 0.8680 (ttt) REVERT: A 299 ASP cc_start: 0.8553 (p0) cc_final: 0.8315 (p0) REVERT: A 381 VAL cc_start: 0.8535 (m) cc_final: 0.8054 (p) REVERT: A 444 GLU cc_start: 0.7850 (pp20) cc_final: 0.6926 (mp0) REVERT: A 456 LEU cc_start: 0.8485 (mt) cc_final: 0.8241 (mt) REVERT: B 74 MET cc_start: 0.5263 (tpp) cc_final: 0.4900 (mmm) REVERT: C 58 LYS cc_start: 0.7973 (mttt) cc_final: 0.6888 (tptt) REVERT: C 66 ASN cc_start: 0.8060 (m-40) cc_final: 0.7682 (t0) REVERT: C 70 PHE cc_start: 0.8822 (p90) cc_final: 0.8477 (p90) REVERT: C 74 PHE cc_start: 0.2265 (OUTLIER) cc_final: 0.1028 (m-10) REVERT: D 139 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8050 (mmtp) REVERT: D 178 ASP cc_start: 0.6543 (t70) cc_final: 0.6252 (t0) REVERT: E 1 MET cc_start: 0.2825 (ttp) cc_final: 0.2229 (ptm) REVERT: E 35 MET cc_start: 0.5497 (tmm) cc_final: 0.5114 (ptp) REVERT: E 83 LEU cc_start: 0.4991 (OUTLIER) cc_final: 0.4709 (mp) REVERT: E 132 GLN cc_start: 0.6918 (mt0) cc_final: 0.6213 (mt0) REVERT: E 136 ARG cc_start: 0.6428 (ttm110) cc_final: 0.5442 (mmt180) REVERT: F 23 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7745 (p) REVERT: F 25 ASP cc_start: 0.7153 (p0) cc_final: 0.6413 (m-30) REVERT: F 125 LYS cc_start: 0.8494 (mmmt) cc_final: 0.7999 (ttmt) REVERT: F 222 ILE cc_start: 0.9163 (mt) cc_final: 0.8881 (mt) REVERT: F 384 MET cc_start: 0.7830 (tpp) cc_final: 0.7596 (mmp) REVERT: F 426 GLN cc_start: 0.7882 (tp40) cc_final: 0.7509 (tp-100) REVERT: F 469 MET cc_start: 0.2886 (mmt) cc_final: 0.2136 (mpp) REVERT: G 25 ASP cc_start: 0.7120 (t0) cc_final: 0.6688 (p0) REVERT: G 109 SER cc_start: 0.8743 (t) cc_final: 0.8513 (p) REVERT: G 128 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7878 (ttp-170) REVERT: G 349 ASP cc_start: 0.7183 (t70) cc_final: 0.6714 (t0) REVERT: G 426 GLN cc_start: 0.7475 (tp40) cc_final: 0.7080 (tp40) REVERT: G 444 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6966 (tm-30) REVERT: H 57 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7866 (mm-30) REVERT: H 92 ASN cc_start: 0.7877 (t0) cc_final: 0.7256 (t0) REVERT: H 171 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7163 (mt) REVERT: H 444 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6223 (tt0) REVERT: I 166 MET cc_start: 0.8969 (mtm) cc_final: 0.8558 (mpp) REVERT: I 426 GLN cc_start: 0.8034 (tp40) cc_final: 0.7320 (pt0) REVERT: I 460 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7586 (mmtt) REVERT: J 23 THR cc_start: 0.7479 (m) cc_final: 0.6925 (p) REVERT: J 76 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7859 (mpp-170) REVERT: J 175 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6504 (mt) REVERT: J 436 ARG cc_start: 0.7023 (tpp80) cc_final: 0.6529 (mtp85) REVERT: K 74 MET cc_start: 0.4864 (tpp) cc_final: 0.4581 (tpt) REVERT: K 279 LYS cc_start: 0.8815 (mttt) cc_final: 0.8569 (mmtp) REVERT: K 435 TYR cc_start: 0.8268 (m-10) cc_final: 0.8041 (m-80) REVERT: L 10 LYS cc_start: 0.5989 (mtmt) cc_final: 0.5662 (mtmt) REVERT: M 38 ILE cc_start: 0.5583 (OUTLIER) cc_final: 0.5329 (pt) REVERT: N 22 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6690 (mm-30) REVERT: N 36 ASN cc_start: 0.6773 (t0) cc_final: 0.6372 (t0) REVERT: N 57 LYS cc_start: 0.6924 (mtmt) cc_final: 0.6652 (mmmt) REVERT: N 66 ASN cc_start: 0.8904 (m110) cc_final: 0.8682 (m-40) REVERT: R 324 MET cc_start: 0.0090 (mmm) cc_final: -0.1497 (ptm) REVERT: S 393 GLU cc_start: 0.0583 (OUTLIER) cc_final: 0.0060 (pp20) outliers start: 101 outliers final: 57 residues processed: 588 average time/residue: 0.2791 time to fit residues: 260.4731 Evaluate side-chains 547 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 483 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 433 ASP Chi-restraints excluded: chain H residue 155 GLU Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 460 LYS Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 189 CYS Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 249 LYS Chi-restraints excluded: chain I residue 342 PHE Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 431 VAL Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 335 VAL Chi-restraints excluded: chain S residue 393 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 95 optimal weight: 1.9990 chunk 198 optimal weight: 0.4980 chunk 475 optimal weight: 9.9990 chunk 413 optimal weight: 6.9990 chunk 411 optimal weight: 8.9990 chunk 412 optimal weight: 1.9990 chunk 433 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 287 optimal weight: 0.9980 chunk 403 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 84 GLN E 113 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 209 GLN K 223 HIS K 291 HIS M 12 ASN P 5 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.166447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133806 restraints weight = 45847.421| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.65 r_work: 0.3183 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 38813 Z= 0.180 Angle : 0.634 10.544 52555 Z= 0.328 Chirality : 0.046 0.235 5642 Planarity : 0.006 0.256 6889 Dihedral : 5.269 58.582 5286 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.10 % Favored : 92.84 % Rotamer: Outliers : 3.04 % Allowed : 17.66 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.80 % 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 aren not related in a simple way. whole: -0.22 (0.12), residues: 4848 helix: 1.61 (0.13), residues: 1744 sheet: -0.10 (0.21), residues: 555 loop : -1.49 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 191 TYR 0.014 0.001 TYR E 41 PHE 0.022 0.002 PHE B 342 TRP 0.020 0.001 TRP G 408 HIS 0.009 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00430 (38804) covalent geometry : angle 0.63417 (52539) SS BOND : bond 0.01286 ( 8) SS BOND : angle 0.99798 ( 16) hydrogen bonds : bond 0.04879 ( 1425) hydrogen bonds : angle 3.96198 ( 4080) Misc. bond : bond 0.00669 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 492 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.5727 (mppt) cc_final: 0.4939 (mttm) REVERT: A 226 GLN cc_start: 0.8619 (tt0) cc_final: 0.8389 (tt0) REVERT: A 381 VAL cc_start: 0.8483 (m) cc_final: 0.8013 (p) REVERT: B 357 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7752 (tpp-160) REVERT: C 58 LYS cc_start: 0.7871 (mttt) cc_final: 0.6848 (tptt) REVERT: C 74 PHE cc_start: 0.2345 (OUTLIER) cc_final: 0.1044 (m-10) REVERT: D 139 LYS cc_start: 0.8465 (mmtm) cc_final: 0.8115 (mmtp) REVERT: D 178 ASP cc_start: 0.6274 (t70) cc_final: 0.6033 (t0) REVERT: E 1 MET cc_start: 0.2954 (ttp) cc_final: 0.2336 (ptm) REVERT: E 35 MET cc_start: 0.5532 (tmm) cc_final: 0.5183 (tmm) REVERT: E 59 GLU cc_start: 0.6789 (tp30) cc_final: 0.6529 (tp30) REVERT: E 105 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6342 (mp0) REVERT: E 132 GLN cc_start: 0.6877 (mt0) cc_final: 0.6248 (mt0) REVERT: E 136 ARG cc_start: 0.6493 (ttm110) cc_final: 0.5356 (mmt180) REVERT: F 23 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7821 (p) REVERT: F 25 ASP cc_start: 0.6951 (p0) cc_final: 0.6390 (m-30) REVERT: F 125 LYS cc_start: 0.8503 (mmmt) cc_final: 0.7960 (ttmt) REVERT: F 222 ILE cc_start: 0.9159 (mt) cc_final: 0.8909 (mm) REVERT: F 384 MET cc_start: 0.7693 (tpp) cc_final: 0.7425 (mmp) REVERT: F 426 GLN cc_start: 0.7872 (tp40) cc_final: 0.7559 (tp40) REVERT: F 469 MET cc_start: 0.2851 (mmt) cc_final: 0.2064 (mpp) REVERT: G 25 ASP cc_start: 0.6988 (t0) cc_final: 0.6558 (p0) REVERT: G 98 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8397 (pt) REVERT: G 109 SER cc_start: 0.8781 (t) cc_final: 0.8535 (p) REVERT: G 298 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8021 (mt) REVERT: G 349 ASP cc_start: 0.7148 (t70) cc_final: 0.6628 (t0) REVERT: G 426 GLN cc_start: 0.7611 (tp40) cc_final: 0.7190 (tp-100) REVERT: G 444 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6918 (tm-30) REVERT: G 463 LYS cc_start: 0.5518 (tptp) cc_final: 0.5249 (tttm) REVERT: H 57 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7823 (mm-30) REVERT: H 125 LYS cc_start: 0.9079 (mmmt) cc_final: 0.8427 (mttm) REVERT: H 171 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7404 (mt) REVERT: H 283 ASP cc_start: 0.7521 (m-30) cc_final: 0.6989 (m-30) REVERT: H 444 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6211 (tt0) REVERT: I 426 GLN cc_start: 0.8023 (tp40) cc_final: 0.7348 (pt0) REVERT: I 448 TRP cc_start: 0.6909 (p-90) cc_final: 0.6464 (p-90) REVERT: I 460 LYS cc_start: 0.8196 (mtpt) cc_final: 0.7608 (mmtt) REVERT: J 23 THR cc_start: 0.7672 (m) cc_final: 0.7364 (p) REVERT: J 49 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: J 57 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7662 (mm-30) REVERT: J 66 VAL cc_start: 0.8828 (m) cc_final: 0.8282 (t) REVERT: J 436 ARG cc_start: 0.7074 (tpp80) cc_final: 0.6591 (mtp85) REVERT: K 74 MET cc_start: 0.4919 (tpp) cc_final: 0.4480 (tpt) REVERT: K 191 ARG cc_start: 0.8012 (ttp-170) cc_final: 0.7701 (ttp-110) REVERT: K 279 LYS cc_start: 0.8823 (mttt) cc_final: 0.8597 (mmtp) REVERT: L 10 LYS cc_start: 0.5957 (mtmt) cc_final: 0.5634 (mtmt) REVERT: N 36 ASN cc_start: 0.6910 (t0) cc_final: 0.6447 (t0) REVERT: N 57 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6684 (mmtm) REVERT: N 58 LYS cc_start: 0.7185 (mtmm) cc_final: 0.6588 (mmtt) REVERT: Q 36 ASN cc_start: 0.6810 (t0) cc_final: 0.6336 (t0) REVERT: R 324 MET cc_start: 0.0236 (mmm) cc_final: -0.1417 (ptm) REVERT: R 342 LYS cc_start: 0.0315 (OUTLIER) cc_final: -0.0145 (mmtt) REVERT: S 295 PHE cc_start: 0.1086 (OUTLIER) cc_final: 0.0545 (m-80) REVERT: S 393 GLU cc_start: 0.0845 (OUTLIER) cc_final: 0.0399 (pp20) outliers start: 120 outliers final: 80 residues processed: 585 average time/residue: 0.2650 time to fit residues: 246.7294 Evaluate side-chains 561 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 470 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 294 MET Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 433 ASP Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 460 LYS Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 189 CYS Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 249 LYS Chi-restraints excluded: chain I residue 299 ASP Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 342 PHE Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 376 SER Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 61 LEU Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 62 CYS Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 371 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 431 VAL Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 327 ILE Chi-restraints excluded: chain S residue 393 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 183 optimal weight: 0.5980 chunk 98 optimal weight: 0.1980 chunk 160 optimal weight: 2.9990 chunk 232 optimal weight: 0.0980 chunk 464 optimal weight: 8.9990 chunk 398 optimal weight: 2.9990 chunk 404 optimal weight: 0.7980 chunk 337 optimal weight: 3.9990 chunk 361 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 395 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 66 ASN E 6 GLN E 84 GLN E 113 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 ASN M 12 ASN R 405 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.172055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.138093 restraints weight = 45216.883| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.54 r_work: 0.3246 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 38813 Z= 0.105 Angle : 0.557 10.830 52555 Z= 0.287 Chirality : 0.042 0.248 5642 Planarity : 0.004 0.067 6889 Dihedral : 4.801 57.752 5277 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.65 % Favored : 94.29 % Rotamer: Outliers : 2.58 % Allowed : 18.37 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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 aren not related in a simple way. whole: 0.11 (0.12), residues: 4848 helix: 1.97 (0.13), residues: 1740 sheet: -0.04 (0.20), residues: 591 loop : -1.33 (0.12), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 191 TYR 0.026 0.001 TYR E 5 PHE 0.018 0.001 PHE H 466 TRP 0.014 0.001 TRP H 408 HIS 0.006 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00232 (38804) covalent geometry : angle 0.55698 (52539) SS BOND : bond 0.00961 ( 8) SS BOND : angle 0.75459 ( 16) hydrogen bonds : bond 0.03232 ( 1425) hydrogen bonds : angle 3.77015 ( 4080) Misc. bond : bond 0.00149 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 488 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8098 (tp30) cc_final: 0.7750 (tp30) REVERT: A 174 LYS cc_start: 0.5529 (mppt) cc_final: 0.4860 (mttm) REVERT: A 226 GLN cc_start: 0.8428 (tt0) cc_final: 0.8196 (tt0) REVERT: A 444 GLU cc_start: 0.7668 (pp20) cc_final: 0.6924 (mp0) REVERT: B 74 MET cc_start: 0.5199 (tpp) cc_final: 0.4818 (mmm) REVERT: B 357 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7706 (tpp-160) REVERT: C 58 LYS cc_start: 0.7869 (mttt) cc_final: 0.6851 (tptt) REVERT: C 74 PHE cc_start: 0.2433 (OUTLIER) cc_final: 0.1267 (m-10) REVERT: D 139 LYS cc_start: 0.8369 (mmtm) cc_final: 0.8070 (mmtp) REVERT: E 35 MET cc_start: 0.5551 (tmm) cc_final: 0.5210 (tmm) REVERT: E 83 LEU cc_start: 0.5005 (OUTLIER) cc_final: 0.4755 (mp) REVERT: E 105 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: E 132 GLN cc_start: 0.6715 (mt0) cc_final: 0.6098 (mt0) REVERT: E 136 ARG cc_start: 0.6477 (ttm110) cc_final: 0.5420 (mmt180) REVERT: F 25 ASP cc_start: 0.6954 (p0) cc_final: 0.6361 (m-30) REVERT: F 125 LYS cc_start: 0.8423 (mmmt) cc_final: 0.7896 (ttmt) REVERT: F 222 ILE cc_start: 0.9143 (mt) cc_final: 0.8862 (mt) REVERT: F 384 MET cc_start: 0.7631 (tpp) cc_final: 0.7394 (mmp) REVERT: F 426 GLN cc_start: 0.7852 (tp40) cc_final: 0.7577 (tp-100) REVERT: F 451 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: F 469 MET cc_start: 0.3048 (mmt) cc_final: 0.1458 (mtp) REVERT: G 25 ASP cc_start: 0.6928 (t0) cc_final: 0.6596 (p0) REVERT: G 109 SER cc_start: 0.8674 (t) cc_final: 0.8415 (p) REVERT: G 128 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7625 (ttp-170) REVERT: G 349 ASP cc_start: 0.7038 (t70) cc_final: 0.6585 (t0) REVERT: G 426 GLN cc_start: 0.7523 (tp40) cc_final: 0.7095 (tp40) REVERT: G 444 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6940 (tm-30) REVERT: G 463 LYS cc_start: 0.5149 (tptp) cc_final: 0.4935 (tttm) REVERT: H 57 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7779 (mm-30) REVERT: H 125 LYS cc_start: 0.9072 (mmmt) cc_final: 0.8426 (mttm) REVERT: H 171 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7227 (mt) REVERT: H 444 GLU cc_start: 0.6537 (mt-10) cc_final: 0.6121 (tt0) REVERT: I 71 LEU cc_start: 0.1748 (OUTLIER) cc_final: 0.1463 (pp) REVERT: I 166 MET cc_start: 0.8948 (mtm) cc_final: 0.8543 (mpp) REVERT: I 426 GLN cc_start: 0.8010 (tp40) cc_final: 0.7351 (pt0) REVERT: I 448 TRP cc_start: 0.6886 (p-90) cc_final: 0.6426 (p-90) REVERT: I 460 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7615 (mmtt) REVERT: J 23 THR cc_start: 0.7431 (m) cc_final: 0.6937 (p) REVERT: J 49 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: J 57 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7595 (mm-30) REVERT: J 66 VAL cc_start: 0.8790 (m) cc_final: 0.8278 (t) REVERT: J 74 MET cc_start: 0.5032 (tpp) cc_final: 0.4811 (tpp) REVERT: J 175 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6427 (mt) REVERT: J 436 ARG cc_start: 0.7021 (tpp80) cc_final: 0.6593 (mtp85) REVERT: K 74 MET cc_start: 0.4872 (tpp) cc_final: 0.4518 (tpt) REVERT: K 206 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7494 (mp10) REVERT: K 279 LYS cc_start: 0.8760 (mttt) cc_final: 0.8526 (mmtp) REVERT: N 36 ASN cc_start: 0.6776 (t0) cc_final: 0.6338 (t0) REVERT: N 58 LYS cc_start: 0.7142 (mtmm) cc_final: 0.6651 (mmtt) REVERT: Q 28 SER cc_start: 0.7752 (t) cc_final: 0.7382 (p) REVERT: Q 57 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7845 (mtpt) REVERT: R 324 MET cc_start: -0.0090 (mmm) cc_final: -0.1868 (ptm) REVERT: R 342 LYS cc_start: 0.0333 (OUTLIER) cc_final: -0.0168 (mmtt) REVERT: S 393 GLU cc_start: 0.0673 (OUTLIER) cc_final: 0.0130 (pp20) outliers start: 102 outliers final: 60 residues processed: 567 average time/residue: 0.2756 time to fit residues: 247.0719 Evaluate side-chains 537 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 466 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 248 MET Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 435 TYR Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 460 LYS Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 249 LYS Chi-restraints excluded: chain I residue 299 ASP Chi-restraints excluded: chain I residue 324 HIS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 342 PHE Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 376 SER Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 206 GLN Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 379 ILE Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 335 VAL Chi-restraints excluded: chain S residue 393 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 387 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 396 optimal weight: 4.9990 chunk 409 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 304 optimal weight: 6.9990 chunk 427 optimal weight: 0.5980 chunk 357 optimal weight: 0.7980 chunk 380 optimal weight: 5.9990 chunk 276 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 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 = 0.3854 r_free = 0.3854 target = 0.167459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133712 restraints weight = 45358.838| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.68 r_work: 0.3172 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 38813 Z= 0.148 Angle : 0.610 13.743 52555 Z= 0.312 Chirality : 0.045 0.270 5642 Planarity : 0.005 0.094 6889 Dihedral : 4.896 52.530 5276 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.01 % Favored : 92.92 % Rotamer: Outliers : 2.45 % Allowed : 18.78 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.35 % 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 aren not related in a simple way. whole: 0.05 (0.12), residues: 4848 helix: 1.82 (0.13), residues: 1752 sheet: 0.02 (0.20), residues: 583 loop : -1.32 (0.13), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 191 TYR 0.014 0.001 TYR E 41 PHE 0.020 0.002 PHE B 342 TRP 0.018 0.001 TRP G 408 HIS 0.008 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00350 (38804) covalent geometry : angle 0.60992 (52539) SS BOND : bond 0.01289 ( 8) SS BOND : angle 0.99242 ( 16) hydrogen bonds : bond 0.04357 ( 1425) hydrogen bonds : angle 3.86834 ( 4080) Misc. bond : bond 0.00885 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 483 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8243 (tp30) cc_final: 0.7966 (tp30) REVERT: A 174 LYS cc_start: 0.5689 (mppt) cc_final: 0.4995 (mttm) REVERT: A 226 GLN cc_start: 0.8619 (tt0) cc_final: 0.8380 (tt0) REVERT: A 444 GLU cc_start: 0.7746 (pp20) cc_final: 0.6914 (mp0) REVERT: A 456 LEU cc_start: 0.8370 (mt) cc_final: 0.8137 (mt) REVERT: B 57 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7463 (tt0) REVERT: C 58 LYS cc_start: 0.7998 (mttt) cc_final: 0.6938 (tptt) REVERT: C 74 PHE cc_start: 0.2584 (OUTLIER) cc_final: 0.1382 (m-10) REVERT: D 139 LYS cc_start: 0.8418 (mmtm) cc_final: 0.8084 (mmtp) REVERT: E 35 MET cc_start: 0.5662 (tmm) cc_final: 0.5456 (tmm) REVERT: E 105 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: E 132 GLN cc_start: 0.6740 (mt0) cc_final: 0.6109 (mt0) REVERT: E 136 ARG cc_start: 0.6549 (ttm110) cc_final: 0.5393 (mmt180) REVERT: F 25 ASP cc_start: 0.6951 (p0) cc_final: 0.6462 (m-30) REVERT: F 57 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7418 (tt0) REVERT: F 125 LYS cc_start: 0.8456 (mmmt) cc_final: 0.7923 (ttmt) REVERT: F 222 ILE cc_start: 0.9119 (mt) cc_final: 0.8846 (mt) REVERT: F 384 MET cc_start: 0.7743 (tpp) cc_final: 0.7486 (mmp) REVERT: F 426 GLN cc_start: 0.7888 (tp40) cc_final: 0.7577 (tp40) REVERT: F 469 MET cc_start: 0.2759 (mmt) cc_final: 0.1274 (mtp) REVERT: G 25 ASP cc_start: 0.6985 (t0) cc_final: 0.6616 (p0) REVERT: G 109 SER cc_start: 0.8716 (t) cc_final: 0.8467 (p) REVERT: G 292 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8370 (ptt180) REVERT: G 349 ASP cc_start: 0.7122 (t70) cc_final: 0.6629 (t0) REVERT: G 426 GLN cc_start: 0.7540 (tp40) cc_final: 0.7104 (tp-100) REVERT: G 444 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6872 (tm-30) REVERT: G 463 LYS cc_start: 0.5570 (tptp) cc_final: 0.5317 (tttm) REVERT: H 57 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7855 (mm-30) REVERT: H 125 LYS cc_start: 0.9112 (mmmt) cc_final: 0.8432 (mttm) REVERT: H 171 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7328 (mt) REVERT: H 283 ASP cc_start: 0.7431 (m-30) cc_final: 0.6895 (m-30) REVERT: H 444 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6189 (tt0) REVERT: I 71 LEU cc_start: 0.1832 (OUTLIER) cc_final: 0.1549 (pp) REVERT: I 166 MET cc_start: 0.9060 (mtm) cc_final: 0.8692 (mpp) REVERT: I 426 GLN cc_start: 0.7995 (tp40) cc_final: 0.7295 (pt0) REVERT: I 448 TRP cc_start: 0.6694 (p-90) cc_final: 0.6336 (p-90) REVERT: I 460 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7643 (mmtt) REVERT: J 23 THR cc_start: 0.7385 (m) cc_final: 0.6910 (p) REVERT: J 49 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: J 66 VAL cc_start: 0.8744 (m) cc_final: 0.8236 (t) REVERT: J 74 MET cc_start: 0.4953 (tpp) cc_final: 0.4741 (tpp) REVERT: J 436 ARG cc_start: 0.7068 (tpp80) cc_final: 0.6607 (mtp85) REVERT: K 191 ARG cc_start: 0.7995 (ttp-170) cc_final: 0.7711 (ttp-110) REVERT: K 206 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7583 (mt0) REVERT: K 279 LYS cc_start: 0.8807 (mttt) cc_final: 0.8586 (mmtp) REVERT: N 36 ASN cc_start: 0.6773 (t0) cc_final: 0.6177 (t0) REVERT: N 58 LYS cc_start: 0.7179 (mtmm) cc_final: 0.6627 (mmtt) REVERT: Q 28 SER cc_start: 0.7851 (t) cc_final: 0.7625 (p) REVERT: Q 36 ASN cc_start: 0.6853 (t0) cc_final: 0.6410 (t0) REVERT: Q 57 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7859 (mtpt) REVERT: R 324 MET cc_start: 0.0261 (mmm) cc_final: -0.1763 (ptm) REVERT: S 295 PHE cc_start: 0.1006 (OUTLIER) cc_final: 0.0293 (m-80) REVERT: S 393 GLU cc_start: 0.0855 (OUTLIER) cc_final: 0.0334 (pp20) outliers start: 97 outliers final: 72 residues processed: 558 average time/residue: 0.2740 time to fit residues: 241.9455 Evaluate side-chains 545 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 464 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 248 MET Chi-restraints excluded: chain G residue 292 ARG Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 435 TYR Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 460 LYS Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 249 LYS Chi-restraints excluded: chain I residue 299 ASP Chi-restraints excluded: chain I residue 324 HIS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 342 PHE Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 376 SER Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 206 GLN Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 379 ILE Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain N residue 70 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 327 ILE Chi-restraints excluded: chain S residue 393 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 36 optimal weight: 1.9990 chunk 352 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 350 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 351 optimal weight: 0.9990 chunk 218 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN B 112 ASN D 175 ASN E 113 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.169270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134653 restraints weight = 45696.149| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.70 r_work: 0.3155 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38813 Z= 0.116 Angle : 0.577 16.505 52555 Z= 0.294 Chirality : 0.043 0.254 5642 Planarity : 0.005 0.201 6889 Dihedral : 5.196 154.115 5276 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.15 % Favored : 93.79 % Rotamer: Outliers : 2.23 % Allowed : 19.13 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.90 % 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 aren not related in a simple way. whole: 0.19 (0.12), residues: 4848 helix: 1.98 (0.13), residues: 1743 sheet: 0.06 (0.20), residues: 583 loop : -1.26 (0.13), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 191 TYR 0.024 0.001 TYR E 5 PHE 0.018 0.001 PHE H 466 TRP 0.015 0.001 TRP G 408 HIS 0.006 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00267 (38804) covalent geometry : angle 0.57714 (52539) SS BOND : bond 0.01135 ( 8) SS BOND : angle 0.78130 ( 16) hydrogen bonds : bond 0.03571 ( 1425) hydrogen bonds : angle 3.78779 ( 4080) Misc. bond : bond 0.00364 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 478 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8143 (tp30) cc_final: 0.7872 (tp30) REVERT: A 92 ASN cc_start: 0.7864 (t0) cc_final: 0.7303 (t0) REVERT: A 174 LYS cc_start: 0.5592 (mppt) cc_final: 0.4860 (mttm) REVERT: A 226 GLN cc_start: 0.8588 (tt0) cc_final: 0.8319 (tt0) REVERT: A 444 GLU cc_start: 0.7696 (pp20) cc_final: 0.6891 (mp0) REVERT: A 456 LEU cc_start: 0.8374 (mt) cc_final: 0.8126 (mt) REVERT: B 74 MET cc_start: 0.5103 (tpp) cc_final: 0.4711 (mmm) REVERT: B 336 LYS cc_start: 0.6090 (ttpt) cc_final: 0.5840 (ttpp) REVERT: C 40 HIS cc_start: 0.4133 (OUTLIER) cc_final: 0.3409 (t-170) REVERT: C 58 LYS cc_start: 0.7986 (mttt) cc_final: 0.6925 (tptt) REVERT: C 74 PHE cc_start: 0.2476 (OUTLIER) cc_final: 0.1338 (m-10) REVERT: D 139 LYS cc_start: 0.8306 (mmtm) cc_final: 0.7978 (mmtp) REVERT: E 1 MET cc_start: 0.2774 (ttm) cc_final: 0.2077 (ptt) REVERT: E 59 GLU cc_start: 0.6546 (tp30) cc_final: 0.6330 (tp30) REVERT: E 83 LEU cc_start: 0.5178 (OUTLIER) cc_final: 0.4681 (mp) REVERT: E 105 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: E 132 GLN cc_start: 0.6639 (mt0) cc_final: 0.6010 (mt0) REVERT: E 136 ARG cc_start: 0.6502 (ttm110) cc_final: 0.5490 (mmt180) REVERT: F 25 ASP cc_start: 0.7000 (p0) cc_final: 0.6423 (m-30) REVERT: F 57 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7317 (tt0) REVERT: F 125 LYS cc_start: 0.8329 (mmmt) cc_final: 0.7847 (ttmt) REVERT: F 222 ILE cc_start: 0.9091 (mt) cc_final: 0.8830 (mt) REVERT: F 384 MET cc_start: 0.7680 (tpp) cc_final: 0.7439 (mmp) REVERT: F 426 GLN cc_start: 0.7853 (tp40) cc_final: 0.7563 (tp40) REVERT: F 451 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: F 469 MET cc_start: 0.2846 (mmt) cc_final: 0.1321 (mtp) REVERT: G 25 ASP cc_start: 0.6958 (t0) cc_final: 0.6609 (p0) REVERT: G 109 SER cc_start: 0.8725 (t) cc_final: 0.8473 (p) REVERT: G 349 ASP cc_start: 0.7014 (t70) cc_final: 0.6566 (t0) REVERT: G 426 GLN cc_start: 0.7489 (tp40) cc_final: 0.7044 (tp40) REVERT: G 444 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6835 (tm-30) REVERT: G 463 LYS cc_start: 0.5275 (tptp) cc_final: 0.5001 (tttm) REVERT: H 57 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7893 (mm-30) REVERT: H 125 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8384 (mttm) REVERT: H 171 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7290 (mt) REVERT: H 283 ASP cc_start: 0.7415 (m-30) cc_final: 0.6879 (m-30) REVERT: H 444 GLU cc_start: 0.6374 (mt-10) cc_final: 0.6084 (tt0) REVERT: H 469 MET cc_start: 0.1599 (tpp) cc_final: 0.1290 (tpp) REVERT: I 71 LEU cc_start: 0.1754 (OUTLIER) cc_final: 0.1420 (pp) REVERT: I 166 MET cc_start: 0.9043 (mtm) cc_final: 0.8695 (mpp) REVERT: I 368 MET cc_start: 0.8109 (ttm) cc_final: 0.7901 (ttt) REVERT: I 426 GLN cc_start: 0.7949 (tp40) cc_final: 0.7259 (pt0) REVERT: I 448 TRP cc_start: 0.6722 (p-90) cc_final: 0.6312 (p-90) REVERT: I 460 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7661 (mmtt) REVERT: J 23 THR cc_start: 0.7262 (m) cc_final: 0.6780 (p) REVERT: J 49 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: J 57 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7640 (mm-30) REVERT: J 66 VAL cc_start: 0.8666 (m) cc_final: 0.8169 (t) REVERT: J 436 ARG cc_start: 0.7090 (tpp80) cc_final: 0.6571 (mtp85) REVERT: K 279 LYS cc_start: 0.8780 (mttt) cc_final: 0.8568 (mmtp) REVERT: K 463 LYS cc_start: 0.6665 (tttm) cc_final: 0.6419 (tmtt) REVERT: N 36 ASN cc_start: 0.6769 (t0) cc_final: 0.6115 (t0) REVERT: N 58 LYS cc_start: 0.7140 (mtmm) cc_final: 0.6612 (mmtt) REVERT: O 65 CYS cc_start: 0.4709 (OUTLIER) cc_final: 0.4213 (p) REVERT: Q 28 SER cc_start: 0.7840 (t) cc_final: 0.7608 (p) REVERT: Q 36 ASN cc_start: 0.6825 (t0) cc_final: 0.6317 (t0) REVERT: R 324 MET cc_start: 0.0210 (mmm) cc_final: -0.1809 (ptm) REVERT: R 342 LYS cc_start: 0.0169 (OUTLIER) cc_final: -0.0290 (mmtt) REVERT: S 318 LYS cc_start: 0.1255 (OUTLIER) cc_final: 0.0730 (ptmm) REVERT: S 393 GLU cc_start: 0.0770 (OUTLIER) cc_final: 0.0246 (pp20) outliers start: 88 outliers final: 69 residues processed: 545 average time/residue: 0.2761 time to fit residues: 237.4042 Evaluate side-chains 546 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 465 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 248 MET Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 435 TYR Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 460 LYS Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 249 LYS Chi-restraints excluded: chain I residue 299 ASP Chi-restraints excluded: chain I residue 324 HIS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 342 PHE Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 376 SER Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 379 ILE Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 65 CYS Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 327 ILE Chi-restraints excluded: chain S residue 393 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 413 optimal weight: 0.7980 chunk 344 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 356 optimal weight: 0.8980 chunk 387 optimal weight: 5.9990 chunk 234 optimal weight: 0.0670 chunk 332 optimal weight: 0.3980 chunk 203 optimal weight: 3.9990 chunk 437 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.172155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137984 restraints weight = 45153.141| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.50 r_work: 0.3220 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 38813 Z= 0.105 Angle : 0.572 16.193 52555 Z= 0.289 Chirality : 0.042 0.254 5642 Planarity : 0.004 0.078 6889 Dihedral : 4.637 50.130 5276 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.17 % Favored : 93.77 % Rotamer: Outliers : 2.20 % Allowed : 19.33 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.90 % 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 aren not related in a simple way. whole: 0.30 (0.13), residues: 4848 helix: 2.10 (0.13), residues: 1749 sheet: 0.09 (0.20), residues: 591 loop : -1.21 (0.13), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.000 ARG A 191 TYR 0.033 0.001 TYR E 5 PHE 0.018 0.001 PHE H 466 TRP 0.013 0.001 TRP H 408 HIS 0.006 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00235 (38804) covalent geometry : angle 0.57197 (52539) SS BOND : bond 0.01044 ( 8) SS BOND : angle 0.70143 ( 16) hydrogen bonds : bond 0.03283 ( 1425) hydrogen bonds : angle 3.71838 ( 4080) Misc. bond : bond 0.00546 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 485 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8118 (tp30) cc_final: 0.7866 (tp30) REVERT: A 92 ASN cc_start: 0.7807 (t0) cc_final: 0.7260 (t0) REVERT: A 174 LYS cc_start: 0.5666 (mppt) cc_final: 0.4894 (mttm) REVERT: A 226 GLN cc_start: 0.8545 (tt0) cc_final: 0.8297 (tt0) REVERT: A 444 GLU cc_start: 0.7700 (pp20) cc_final: 0.6797 (mp0) REVERT: A 456 LEU cc_start: 0.8317 (mt) cc_final: 0.8074 (mt) REVERT: B 74 MET cc_start: 0.5024 (tpp) cc_final: 0.4648 (mmm) REVERT: B 228 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6666 (mm-30) REVERT: B 252 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7344 (mm-30) REVERT: B 336 LYS cc_start: 0.6162 (ttpt) cc_final: 0.5898 (ttpp) REVERT: C 40 HIS cc_start: 0.4116 (OUTLIER) cc_final: 0.3288 (t-170) REVERT: C 58 LYS cc_start: 0.7966 (mttt) cc_final: 0.6882 (tptt) REVERT: C 66 ASN cc_start: 0.8880 (t0) cc_final: 0.8372 (t0) REVERT: C 74 PHE cc_start: 0.2374 (OUTLIER) cc_final: 0.1224 (m-10) REVERT: D 172 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6957 (tm-30) REVERT: E 1 MET cc_start: 0.2644 (ttm) cc_final: 0.1979 (ptt) REVERT: E 83 LEU cc_start: 0.5210 (OUTLIER) cc_final: 0.4738 (mp) REVERT: E 105 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: E 132 GLN cc_start: 0.6563 (mt0) cc_final: 0.5955 (mt0) REVERT: E 136 ARG cc_start: 0.6541 (ttm110) cc_final: 0.5607 (mmt180) REVERT: F 25 ASP cc_start: 0.6907 (p0) cc_final: 0.6453 (m-30) REVERT: F 57 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7356 (tt0) REVERT: F 125 LYS cc_start: 0.8304 (mmmt) cc_final: 0.7853 (ttmt) REVERT: F 222 ILE cc_start: 0.9085 (mt) cc_final: 0.8819 (mt) REVERT: F 384 MET cc_start: 0.7663 (tpp) cc_final: 0.7422 (mmp) REVERT: F 426 GLN cc_start: 0.7820 (tp40) cc_final: 0.7532 (tp40) REVERT: F 451 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: F 469 MET cc_start: 0.2709 (mmt) cc_final: 0.1291 (mtp) REVERT: G 25 ASP cc_start: 0.6877 (t0) cc_final: 0.6582 (p0) REVERT: G 109 SER cc_start: 0.8682 (t) cc_final: 0.8420 (p) REVERT: G 292 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8311 (ptt180) REVERT: G 349 ASP cc_start: 0.6903 (t70) cc_final: 0.6498 (t0) REVERT: G 426 GLN cc_start: 0.7470 (tp40) cc_final: 0.7030 (tp40) REVERT: G 444 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6819 (tm-30) REVERT: G 463 LYS cc_start: 0.5317 (tptp) cc_final: 0.5044 (tttm) REVERT: H 125 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8406 (mttm) REVERT: H 171 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7260 (mt) REVERT: H 444 GLU cc_start: 0.6413 (mt-10) cc_final: 0.6111 (tt0) REVERT: H 469 MET cc_start: 0.1642 (tpp) cc_final: 0.1373 (tpp) REVERT: I 71 LEU cc_start: 0.1798 (OUTLIER) cc_final: 0.1520 (pp) REVERT: I 166 MET cc_start: 0.8979 (mtm) cc_final: 0.8607 (mpp) REVERT: I 426 GLN cc_start: 0.7946 (tp40) cc_final: 0.7276 (pt0) REVERT: I 460 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7671 (mmtt) REVERT: J 23 THR cc_start: 0.7268 (m) cc_final: 0.6801 (p) REVERT: J 49 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: J 66 VAL cc_start: 0.8711 (m) cc_final: 0.8197 (t) REVERT: J 436 ARG cc_start: 0.7013 (tpp80) cc_final: 0.6575 (mtp85) REVERT: K 191 ARG cc_start: 0.7864 (ttp-170) cc_final: 0.7609 (ttp-110) REVERT: K 206 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7419 (mt0) REVERT: N 36 ASN cc_start: 0.6733 (t0) cc_final: 0.6067 (t0) REVERT: N 58 LYS cc_start: 0.7125 (mtmm) cc_final: 0.6584 (mmtt) REVERT: O 65 CYS cc_start: 0.4518 (OUTLIER) cc_final: 0.4054 (p) REVERT: Q 36 ASN cc_start: 0.7124 (t0) cc_final: 0.6597 (t0) REVERT: R 324 MET cc_start: 0.0264 (mmm) cc_final: -0.1510 (ptm) REVERT: R 342 LYS cc_start: 0.0145 (OUTLIER) cc_final: -0.0217 (mmtt) REVERT: S 295 PHE cc_start: 0.0838 (OUTLIER) cc_final: 0.0261 (m-80) REVERT: S 318 LYS cc_start: 0.1070 (OUTLIER) cc_final: 0.0666 (ptmm) REVERT: S 393 GLU cc_start: 0.0884 (OUTLIER) cc_final: 0.0451 (pp20) outliers start: 87 outliers final: 66 residues processed: 550 average time/residue: 0.2687 time to fit residues: 233.2491 Evaluate side-chains 554 residues out of total 3965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 473 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain G residue 248 MET Chi-restraints excluded: chain G residue 292 ARG Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 342 PHE Chi-restraints excluded: chain G residue 435 TYR Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 342 PHE Chi-restraints excluded: chain H residue 460 LYS Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 249 LYS Chi-restraints excluded: chain I residue 299 ASP Chi-restraints excluded: chain I residue 324 HIS Chi-restraints excluded: chain I residue 325 SER Chi-restraints excluded: chain I residue 342 PHE Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 120 ASN Chi-restraints excluded: chain J residue 155 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 376 SER Chi-restraints excluded: chain J residue 379 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 169 CYS Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 206 GLN Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 379 ILE Chi-restraints excluded: chain K residue 424 CYS Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 GLU Chi-restraints excluded: chain N residue 12 ASN Chi-restraints excluded: chain N residue 62 CYS Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 65 CYS Chi-restraints excluded: chain Q residue 70 PHE Chi-restraints excluded: chain R residue 342 LYS Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain S residue 290 VAL Chi-restraints excluded: chain S residue 295 PHE Chi-restraints excluded: chain S residue 317 LYS Chi-restraints excluded: chain S residue 318 LYS Chi-restraints excluded: chain S residue 393 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 124 optimal weight: 3.9990 chunk 166 optimal weight: 0.0000 chunk 459 optimal weight: 0.3980 chunk 128 optimal weight: 0.9990 chunk 426 optimal weight: 1.9990 chunk 394 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 439 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 chunk 453 optimal weight: 9.9990 overall best weight: 1.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN E 18 GLN F 202 ASN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.169602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.135692 restraints weight = 45379.453| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.59 r_work: 0.3183 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 38813 Z= 0.151 Angle : 0.626 19.143 52555 Z= 0.317 Chirality : 0.045 0.267 5642 Planarity : 0.006 0.338 6889 Dihedral : 4.814 57.046 5274 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.93 % Favored : 93.01 % Rotamer: Outliers : 2.35 % Allowed : 19.31 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.90 % 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 aren not related in a simple way. whole: 0.14 (0.12), residues: 4848 helix: 1.90 (0.13), residues: 1747 sheet: 0.08 (0.20), residues: 578 loop : -1.27 (0.13), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.001 ARG A 191 TYR 0.015 0.001 TYR E 41 PHE 0.020 0.002 PHE B 342 TRP 0.017 0.001 TRP G 408 HIS 0.007 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00360 (38804) covalent geometry : angle 0.62560 (52539) SS BOND : bond 0.01205 ( 8) SS BOND : angle 0.92235 ( 16) hydrogen bonds : bond 0.04331 ( 1425) hydrogen bonds : angle 3.85377 ( 4080) Misc. bond : bond 0.01243 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10950.60 seconds wall clock time: 188 minutes 10.78 seconds (11290.78 seconds total)