Starting phenix.real_space_refine on Fri Jan 16 11:04:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io2_35605/01_2026/8io2_35605_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io2_35605/01_2026/8io2_35605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8io2_35605/01_2026/8io2_35605_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io2_35605/01_2026/8io2_35605_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8io2_35605/01_2026/8io2_35605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io2_35605/01_2026/8io2_35605.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 159 5.16 5 C 23317 2.51 5 N 6426 2.21 5 O 6722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 251 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36624 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3250 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 393} Chain breaks: 5 Chain: "B" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3265 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 396} Chain breaks: 3 Chain: "C" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3253 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 21, 'TRANS': 394} Chain breaks: 4 Chain: "D" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 394} Chain breaks: 5 Chain: "E" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3250 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 393} Chain breaks: 5 Chain: "F" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3265 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 396} Chain breaks: 3 Chain: "G" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3253 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 21, 'TRANS': 394} Chain breaks: 4 Chain: "H" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 394} Chain breaks: 5 Chain: "I" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1536 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "J" 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: "K" 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: "L" 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: "M" 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 Chain: "N" 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 Chain: "O" 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 Chain: "P" 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: "Q" 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: 8.87, per 1000 atoms: 0.24 Number of scatterers: 36624 At special positions: 0 Unit cell: (196.04, 219.96, 151.32, 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 159 16.00 O 6722 8.00 N 6426 7.00 C 23317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS E 244 " - pdb=" SG CYS F 244 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.2 seconds 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8604 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 44 sheets defined 43.2% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 150 through 160 removed outlier: 4.338A pdb=" N VAL A 154 " --> pdb=" O HIS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 192 Processing helix chain 'A' and resid 210 through 224 Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.619A pdb=" N ARG A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.552A pdb=" N LEU A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 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 392 Processing helix chain 'A' and resid 410 through 431 Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 109 through 119 Processing helix chain 'B' and resid 120 through 124 removed outlier: 4.373A pdb=" N PHE B 124 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 150 through 160 removed outlier: 4.333A pdb=" N VAL B 154 " --> pdb=" O HIS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 210 through 228 Processing helix chain 'B' and resid 243 through 257 Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 294 through 300 removed outlier: 3.920A pdb=" N ILE B 298 " --> pdb=" O MET B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.560A pdb=" N LEU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 346 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 392 Processing helix chain 'B' and resid 409 through 431 Processing helix chain 'B' and resid 437 through 449 Processing helix chain 'B' and resid 449 through 456 Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 109 through 119 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 150 through 160 removed outlier: 4.303A pdb=" N VAL C 154 " --> pdb=" O HIS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 192 Processing helix chain 'C' and resid 210 through 230 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 270 through 285 Processing helix chain 'C' and resid 294 through 300 removed outlier: 4.111A pdb=" N ILE C 298 " --> pdb=" O MET C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.570A pdb=" N LEU C 311 " --> pdb=" O HIS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 392 Processing helix chain 'C' and resid 409 through 430 Processing helix chain 'C' and resid 437 through 446 Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'D' and resid 46 through 58 Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 178 through 192 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 243 through 257 Processing helix chain 'D' and resid 270 through 285 Processing helix chain 'D' and resid 294 through 300 removed outlier: 3.887A pdb=" N ILE D 298 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.544A pdb=" N LEU D 311 " --> pdb=" O HIS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 348 Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 392 Processing helix chain 'D' and resid 411 through 431 Processing helix chain 'D' and resid 437 through 446 Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'E' and resid 46 through 58 Processing helix chain 'E' and resid 73 through 77 Processing helix chain 'E' and resid 101 through 105 Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 150 through 160 removed outlier: 4.338A pdb=" N VAL E 154 " --> pdb=" O HIS E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 192 Processing helix chain 'E' and resid 210 through 224 Processing helix chain 'E' and resid 243 through 257 Processing helix chain 'E' and resid 265 through 270 Processing helix chain 'E' and resid 270 through 285 Processing helix chain 'E' and resid 295 through 300 removed outlier: 3.620A pdb=" N ARG E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 319 removed outlier: 3.552A pdb=" N LEU E 311 " --> pdb=" O HIS E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 346 Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 392 Processing helix chain 'E' and resid 410 through 429 Processing helix chain 'E' and resid 437 through 442 Processing helix chain 'E' and resid 450 through 459 Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 109 through 119 Processing helix chain 'F' and resid 120 through 124 removed outlier: 4.373A pdb=" N PHE F 124 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 143 Processing helix chain 'F' and resid 150 through 160 removed outlier: 4.333A pdb=" N VAL F 154 " --> pdb=" O HIS F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 192 Processing helix chain 'F' and resid 210 through 228 Processing helix chain 'F' and resid 243 through 257 Processing helix chain 'F' and resid 270 through 285 Processing helix chain 'F' and resid 294 through 300 removed outlier: 3.920A pdb=" N ILE F 298 " --> pdb=" O MET F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 319 removed outlier: 3.560A pdb=" N LEU F 311 " --> pdb=" O HIS F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 346 Processing helix chain 'F' and resid 354 through 358 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 392 Processing helix chain 'F' and resid 409 through 430 Processing helix chain 'F' and resid 437 through 447 Processing helix chain 'F' and resid 449 through 456 Processing helix chain 'G' and resid 46 through 58 Processing helix chain 'G' and resid 101 through 105 Processing helix chain 'G' and resid 109 through 119 Processing helix chain 'G' and resid 120 through 124 Processing helix chain 'G' and resid 138 through 143 Processing helix chain 'G' and resid 150 through 160 removed outlier: 4.303A pdb=" N VAL G 154 " --> pdb=" O HIS G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 192 Processing helix chain 'G' and resid 210 through 230 Processing helix chain 'G' and resid 243 through 257 Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 270 through 285 Processing helix chain 'G' and resid 294 through 300 removed outlier: 4.111A pdb=" N ILE G 298 " --> pdb=" O MET G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 319 removed outlier: 3.570A pdb=" N LEU G 311 " --> pdb=" O HIS G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 346 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 Processing helix chain 'G' and resid 409 through 430 Processing helix chain 'G' and resid 437 through 446 Processing helix chain 'G' and resid 449 through 457 Processing helix chain 'H' and resid 46 through 58 Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 109 through 119 Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'H' and resid 138 through 143 Processing helix chain 'H' and resid 151 through 160 Processing helix chain 'H' and resid 178 through 192 Processing helix chain 'H' and resid 210 through 230 Processing helix chain 'H' and resid 243 through 257 Processing helix chain 'H' and resid 270 through 285 Processing helix chain 'H' and resid 294 through 300 removed outlier: 3.887A pdb=" N ILE H 298 " --> pdb=" O MET H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 319 removed outlier: 3.544A pdb=" N LEU H 311 " --> pdb=" O HIS H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 348 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 392 Processing helix chain 'H' and resid 411 through 431 Processing helix chain 'H' and resid 437 through 446 Processing helix chain 'H' and resid 449 through 457 Processing helix chain 'I' and resid 23 through 33 Processing helix chain 'I' and resid 37 through 51 Proline residue: I 43 - end of helix removed outlier: 3.718A pdb=" N SER I 46 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR I 50 " --> pdb=" O SER I 46 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP I 51 " --> pdb=" O SER I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 61 removed outlier: 3.606A pdb=" N GLU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 84 Processing helix chain 'I' and resid 88 through 93 removed outlier: 4.607A pdb=" N ILE I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 104 Processing helix chain 'I' and resid 105 through 109 removed outlier: 4.212A pdb=" N LEU I 108 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 124 removed outlier: 4.138A pdb=" N VAL I 115 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA I 116 " --> pdb=" O THR I 112 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR I 119 " --> pdb=" O VAL I 115 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE I 120 " --> pdb=" O ALA I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 141 Processing helix chain 'I' and resid 142 through 144 No H-bonds generated for 'chain 'I' and resid 142 through 144' Processing helix chain 'I' and resid 157 through 172 removed outlier: 4.544A pdb=" N GLU I 172 " --> pdb=" O ARG I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 189 Processing helix chain 'I' and resid 194 through 205 Processing helix chain 'J' and resid 315 through 322 removed outlier: 3.653A pdb=" N ILE J 319 " --> pdb=" O GLY J 315 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 357 removed outlier: 4.218A pdb=" N GLY J 357 " --> pdb=" O VAL J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 412 through 418 Processing helix chain 'K' and resid 315 through 322 removed outlier: 3.654A pdb=" N ILE K 319 " --> pdb=" O GLY K 315 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 357 removed outlier: 4.218A pdb=" N GLY K 357 " --> pdb=" O VAL K 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 418 Processing helix chain 'L' and resid 315 through 322 removed outlier: 3.653A pdb=" N ILE L 319 " --> pdb=" O GLY L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 357 removed outlier: 4.217A pdb=" N GLY L 357 " --> pdb=" O VAL L 353 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 418 Processing helix chain 'M' and resid 315 through 322 removed outlier: 3.603A pdb=" N ILE M 319 " --> pdb=" O GLY M 315 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 357 removed outlier: 3.553A pdb=" N ILE M 356 " --> pdb=" O PRO M 352 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY M 357 " --> pdb=" O VAL M 353 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 372 removed outlier: 4.262A pdb=" N VAL M 371 " --> pdb=" O ASP M 367 " (cutoff:3.500A) Processing helix chain 'M' and resid 388 through 390 No H-bonds generated for 'chain 'M' and resid 388 through 390' Processing helix chain 'M' and resid 412 through 418 Processing helix chain 'N' and resid 315 through 322 removed outlier: 3.603A pdb=" N ILE N 319 " --> pdb=" O GLY N 315 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 357 removed outlier: 3.552A pdb=" N ILE N 356 " --> pdb=" O PRO N 352 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY N 357 " --> pdb=" O VAL N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 372 removed outlier: 4.262A pdb=" N VAL N 371 " --> pdb=" O ASP N 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 388 through 390 No H-bonds generated for 'chain 'N' and resid 388 through 390' Processing helix chain 'N' and resid 412 through 418 Processing helix chain 'O' and resid 315 through 322 removed outlier: 3.604A pdb=" N ILE O 319 " --> pdb=" O GLY O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 350 through 357 removed outlier: 3.553A pdb=" N ILE O 356 " --> pdb=" O PRO O 352 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY O 357 " --> pdb=" O VAL O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 367 through 372 removed outlier: 4.261A pdb=" N VAL O 371 " --> pdb=" O ASP O 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 388 through 390 No H-bonds generated for 'chain 'O' and resid 388 through 390' Processing helix chain 'O' and resid 412 through 418 Processing helix chain 'P' and resid 315 through 322 removed outlier: 3.653A pdb=" N ILE P 319 " --> pdb=" O GLY P 315 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 357 removed outlier: 4.218A pdb=" N GLY P 357 " --> pdb=" O VAL P 353 " (cutoff:3.500A) Processing helix chain 'P' and resid 412 through 418 Processing helix chain 'Q' and resid 315 through 322 removed outlier: 3.603A pdb=" N ILE Q 319 " --> pdb=" O GLY Q 315 " (cutoff:3.500A) Processing helix chain 'Q' and resid 350 through 357 removed outlier: 3.552A pdb=" N ILE Q 356 " --> pdb=" O PRO Q 352 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY Q 357 " --> pdb=" O VAL Q 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 367 through 372 removed outlier: 4.261A pdb=" N VAL Q 371 " --> pdb=" O ASP Q 367 " (cutoff:3.500A) Processing helix chain 'Q' and resid 388 through 390 No H-bonds generated for 'chain 'Q' and resid 388 through 390' Processing helix chain 'Q' and resid 412 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 86 removed outlier: 5.530A pdb=" N CYS A 81 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA A 99 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 34 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 135 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA A 36 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 170 removed outlier: 6.711A pdb=" N LEU A 167 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LYS A 198 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N CYS A 169 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR A 197 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASN A 238 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N HIS A 235 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N MET A 263 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A 237 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 262 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLN A 398 " --> pdb=" O PRO A 373 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA A 375 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET A 166 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N PHE A 399 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY A 168 " --> pdb=" O PHE A 399 " (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: 6.597A pdb=" N PHE B 97 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 34 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP B 134 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA B 36 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU B 132 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG B 38 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU B 130 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER B 40 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 166 through 170 removed outlier: 6.750A pdb=" N LEU B 167 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LYS B 198 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS B 169 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N THR B 197 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ASN B 238 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N HIS B 235 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N MET B 263 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU B 237 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ASP B 265 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 262 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N HIS B 291 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS B 264 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 323 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N SER B 376 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET B 166 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE B 399 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY B 168 " --> pdb=" O PHE B 399 " (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 80 through 86 removed outlier: 5.577A pdb=" N CYS C 81 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA C 99 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU C 34 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE C 135 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA C 36 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 129 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 166 through 170 removed outlier: 6.713A pdb=" N LEU C 167 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LYS C 198 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYS C 169 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR C 197 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASN C 238 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N HIS C 235 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N MET C 263 " --> pdb=" O HIS C 235 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU C 237 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ASP C 265 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 262 " --> pdb=" O HIS C 289 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N HIS C 291 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS C 264 " --> pdb=" O HIS C 291 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLN C 398 " --> pdb=" O PRO C 373 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA C 375 " --> pdb=" O GLN C 398 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET C 166 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE C 399 " --> pdb=" O MET C 166 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY C 168 " --> pdb=" O PHE C 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB1, first strand: chain 'D' and resid 80 through 86 removed outlier: 5.629A pdb=" N CYS D 81 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA D 99 " --> pdb=" O CYS D 81 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS D 83 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU D 34 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP D 134 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA D 36 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU D 132 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG D 38 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU D 130 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER D 40 " --> pdb=" O ARG D 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 166 through 170 removed outlier: 6.669A pdb=" N LEU D 167 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LYS D 198 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS D 169 " --> pdb=" O LYS D 198 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR D 197 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN D 238 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N HIS D 235 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N MET D 263 " --> pdb=" O HIS D 235 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU D 237 " --> pdb=" O MET D 263 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ASP D 265 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE D 262 " --> pdb=" O HIS D 289 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N HIS D 291 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS D 264 " --> pdb=" O HIS D 291 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU D 323 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N SER D 376 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET D 166 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE D 399 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY D 168 " --> pdb=" O PHE D 399 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 350 through 351 Processing sheet with id=AB4, first strand: chain 'E' and resid 80 through 86 removed outlier: 5.530A pdb=" N CYS E 81 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA E 99 " --> pdb=" O CYS E 81 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU E 34 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE E 135 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA E 36 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 166 through 170 removed outlier: 6.711A pdb=" N LEU E 167 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LYS E 198 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N CYS E 169 " --> pdb=" O LYS E 198 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR E 197 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASN E 238 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N HIS E 235 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N MET E 263 " --> pdb=" O HIS E 235 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU E 237 " --> pdb=" O MET E 263 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE E 262 " --> pdb=" O HIS E 289 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLN E 398 " --> pdb=" O PRO E 373 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA E 375 " --> pdb=" O GLN E 398 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET E 166 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N PHE E 399 " --> pdb=" O MET E 166 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY E 168 " --> pdb=" O PHE E 399 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AB7, first strand: chain 'F' and resid 80 through 83 removed outlier: 6.597A pdb=" N PHE F 97 " --> pdb=" O TYR F 82 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU F 34 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP F 134 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA F 36 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU F 132 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG F 38 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU F 130 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER F 40 " --> pdb=" O ARG F 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 166 through 170 removed outlier: 6.749A pdb=" N LEU F 167 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LYS F 198 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS F 169 " --> pdb=" O LYS F 198 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N THR F 197 " --> pdb=" O TYR F 236 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ASN F 238 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N HIS F 235 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N MET F 263 " --> pdb=" O HIS F 235 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU F 237 " --> pdb=" O MET F 263 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ASP F 265 " --> pdb=" O LEU F 237 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE F 262 " --> pdb=" O HIS F 289 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N HIS F 291 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS F 264 " --> pdb=" O HIS F 291 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU F 323 " --> pdb=" O VAL F 374 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER F 376 " --> pdb=" O LEU F 323 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET F 166 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE F 399 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY F 168 " --> pdb=" O PHE F 399 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 350 through 351 Processing sheet with id=AC1, first strand: chain 'G' and resid 80 through 86 removed outlier: 5.577A pdb=" N CYS G 81 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA G 99 " --> pdb=" O CYS G 81 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU G 34 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE G 135 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA G 36 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER G 129 " --> pdb=" O SER G 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 166 through 170 removed outlier: 6.713A pdb=" N LEU G 167 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LYS G 198 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N CYS G 169 " --> pdb=" O LYS G 198 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR G 197 " --> pdb=" O TYR G 236 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASN G 238 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N HIS G 235 " --> pdb=" O ILE G 261 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N MET G 263 " --> pdb=" O HIS G 235 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU G 237 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ASP G 265 " --> pdb=" O LEU G 237 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE G 262 " --> pdb=" O HIS G 289 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N HIS G 291 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS G 264 " --> pdb=" O HIS G 291 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLN G 398 " --> pdb=" O PRO G 373 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA G 375 " --> pdb=" O GLN G 398 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET G 166 " --> pdb=" O LEU G 397 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE G 399 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY G 168 " --> pdb=" O PHE G 399 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 350 through 351 Processing sheet with id=AC4, first strand: chain 'H' and resid 80 through 86 removed outlier: 5.629A pdb=" N CYS H 81 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA H 99 " --> pdb=" O CYS H 81 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS H 83 " --> pdb=" O PHE H 97 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU H 34 " --> pdb=" O ASP H 134 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASP H 134 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA H 36 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU H 132 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG H 38 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU H 130 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER H 40 " --> pdb=" O ARG H 128 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 166 through 170 removed outlier: 6.669A pdb=" N LEU H 167 " --> pdb=" O PHE H 196 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LYS H 198 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS H 169 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR H 197 " --> pdb=" O TYR H 236 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN H 238 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N HIS H 235 " --> pdb=" O ILE H 261 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N MET H 263 " --> pdb=" O HIS H 235 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU H 237 " --> pdb=" O MET H 263 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ASP H 265 " --> pdb=" O LEU H 237 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE H 262 " --> pdb=" O HIS H 289 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N HIS H 291 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS H 264 " --> pdb=" O HIS H 291 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU H 323 " --> pdb=" O VAL H 374 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N SER H 376 " --> pdb=" O LEU H 323 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET H 166 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE H 399 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY H 168 " --> pdb=" O PHE H 399 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 350 through 351 Processing sheet with id=AC7, first strand: chain 'J' and resid 344 through 345 removed outlier: 3.721A pdb=" N GLY J 425 " --> pdb=" O LEU J 400 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TYR J 398 " --> pdb=" O VAL J 427 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 326 through 328 Processing sheet with id=AC9, first strand: chain 'K' and resid 344 through 345 removed outlier: 3.789A pdb=" N GLY K 425 " --> pdb=" O LEU K 400 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR K 398 " --> pdb=" O VAL K 427 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 326 through 328 Processing sheet with id=AD2, first strand: chain 'L' and resid 344 through 346 removed outlier: 6.360A pdb=" N GLY L 360 " --> pdb=" O VAL L 306 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY L 425 " --> pdb=" O LEU L 400 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR L 398 " --> pdb=" O VAL L 427 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 326 through 328 Processing sheet with id=AD4, first strand: chain 'M' and resid 290 through 292 removed outlier: 3.672A pdb=" N ARG M 432 " --> pdb=" O VAL M 291 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL M 427 " --> pdb=" O ASP M 386 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP M 386 " --> pdb=" O VAL M 427 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU M 429 " --> pdb=" O VAL M 384 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY M 360 " --> pdb=" O VAL M 306 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 290 through 292 removed outlier: 3.672A pdb=" N ARG M 432 " --> pdb=" O VAL M 291 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY M 425 " --> pdb=" O LEU M 400 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TYR M 398 " --> pdb=" O VAL M 427 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 326 through 328 Processing sheet with id=AD7, first strand: chain 'N' and resid 290 through 292 removed outlier: 3.686A pdb=" N ARG N 432 " --> pdb=" O VAL N 291 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL N 427 " --> pdb=" O ASP N 386 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP N 386 " --> pdb=" O VAL N 427 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU N 429 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLY N 360 " --> pdb=" O VAL N 306 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 290 through 292 removed outlier: 3.686A pdb=" N ARG N 432 " --> pdb=" O VAL N 291 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY N 425 " --> pdb=" O LEU N 400 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR N 398 " --> pdb=" O VAL N 427 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 326 through 328 Processing sheet with id=AE1, first strand: chain 'O' and resid 290 through 292 removed outlier: 3.692A pdb=" N ARG O 432 " --> pdb=" O VAL O 291 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL O 427 " --> pdb=" O ASP O 386 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP O 386 " --> pdb=" O VAL O 427 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU O 429 " --> pdb=" O VAL O 384 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY O 360 " --> pdb=" O VAL O 306 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 290 through 292 removed outlier: 3.692A pdb=" N ARG O 432 " --> pdb=" O VAL O 291 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY O 425 " --> pdb=" O LEU O 400 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR O 398 " --> pdb=" O VAL O 427 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 326 through 328 Processing sheet with id=AE4, first strand: chain 'P' and resid 344 through 345 removed outlier: 3.721A pdb=" N GLY P 425 " --> pdb=" O LEU P 400 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR P 398 " --> pdb=" O VAL P 427 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 326 through 328 Processing sheet with id=AE6, first strand: chain 'Q' and resid 290 through 292 removed outlier: 3.686A pdb=" N ARG Q 432 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL Q 427 " --> pdb=" O ASP Q 386 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP Q 386 " --> pdb=" O VAL Q 427 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU Q 429 " --> pdb=" O VAL Q 384 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY Q 360 " --> pdb=" O VAL Q 306 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 290 through 292 removed outlier: 3.686A pdb=" N ARG Q 432 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY Q 425 " --> pdb=" O LEU Q 400 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR Q 398 " --> pdb=" O VAL Q 427 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 326 through 328 1582 hydrogen bonds defined for protein. 4422 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: 9.24 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.51: 25807 1.51 - 1.84: 11633 1.84 - 2.18: 0 2.18 - 2.51: 0 2.51 - 2.85: 4 Bond restraints: 37444 Sorted by residual: bond pdb=" C ASP L 367 " pdb=" N ARG L 369 " ideal model delta sigma weight residual 1.329 2.849 -1.520 1.40e-02 5.10e+03 1.18e+04 bond pdb=" C ASP K 367 " pdb=" N ARG K 369 " ideal model delta sigma weight residual 1.329 2.848 -1.519 1.40e-02 5.10e+03 1.18e+04 bond pdb=" C ASP P 367 " pdb=" N ARG P 369 " ideal model delta sigma weight residual 1.329 2.848 -1.519 1.40e-02 5.10e+03 1.18e+04 bond pdb=" C ASP J 367 " pdb=" N ARG J 369 " ideal model delta sigma weight residual 1.329 2.847 -1.518 1.40e-02 5.10e+03 1.18e+04 bond pdb=" CB PHE H 342 " pdb=" CG PHE H 342 " ideal model delta sigma weight residual 1.502 1.305 0.197 2.30e-02 1.89e+03 7.35e+01 ... (remaining 37439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.79: 50204 5.79 - 11.58: 469 11.58 - 17.37: 47 17.37 - 23.16: 6 23.16 - 28.95: 6 Bond angle restraints: 50732 Sorted by residual: angle pdb=" N VAL P 431 " pdb=" CA VAL P 431 " pdb=" C VAL P 431 " ideal model delta sigma weight residual 110.74 138.82 -28.08 9.10e-01 1.21e+00 9.52e+02 angle pdb=" N VAL L 431 " pdb=" CA VAL L 431 " pdb=" C VAL L 431 " ideal model delta sigma weight residual 110.74 138.79 -28.05 9.10e-01 1.21e+00 9.50e+02 angle pdb=" N VAL J 431 " pdb=" CA VAL J 431 " pdb=" C VAL J 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 P 298 " pdb=" CA VAL P 298 " pdb=" C VAL P 298 " ideal model delta sigma weight residual 107.99 80.04 27.95 1.46e+00 4.69e-01 3.67e+02 angle pdb=" N THR P 302 " pdb=" CA THR P 302 " pdb=" C THR P 302 " ideal model delta sigma weight residual 107.41 136.36 -28.95 2.02e+00 2.45e-01 2.05e+02 ... (remaining 50727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 20351 17.96 - 35.92: 1136 35.92 - 53.88: 542 53.88 - 71.84: 207 71.84 - 89.79: 33 Dihedral angle restraints: 22269 sinusoidal: 8873 harmonic: 13396 Sorted by residual: dihedral pdb=" C GLU P 300 " pdb=" N GLU P 300 " pdb=" CA GLU P 300 " pdb=" CB GLU P 300 " ideal model delta harmonic sigma weight residual -122.60 -160.44 37.84 0 2.50e+00 1.60e-01 2.29e+02 dihedral pdb=" N GLU P 300 " pdb=" C GLU P 300 " pdb=" CA GLU P 300 " pdb=" CB GLU P 300 " ideal model delta harmonic sigma weight residual 122.80 158.13 -35.33 0 2.50e+00 1.60e-01 2.00e+02 dihedral pdb=" N ALA J 301 " pdb=" C ALA J 301 " pdb=" CA ALA J 301 " pdb=" CB ALA J 301 " ideal model delta harmonic sigma weight residual 122.90 154.11 -31.21 0 2.50e+00 1.60e-01 1.56e+02 ... (remaining 22266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.299: 5508 0.299 - 0.598: 46 0.598 - 0.897: 3 0.897 - 1.196: 0 1.196 - 1.495: 4 Chirality restraints: 5561 Sorted by residual: chirality pdb=" CA GLU P 300 " pdb=" N GLU P 300 " pdb=" C GLU P 300 " pdb=" CB GLU P 300 " both_signs ideal model delta sigma weight residual False 2.51 1.02 1.50 2.00e-01 2.50e+01 5.59e+01 chirality pdb=" CA ALA J 301 " pdb=" N ALA J 301 " pdb=" C ALA J 301 " pdb=" CB ALA J 301 " both_signs ideal model delta sigma weight residual False 2.48 1.08 1.40 2.00e-01 2.50e+01 4.91e+01 chirality pdb=" CA ALA L 301 " pdb=" N ALA L 301 " pdb=" C ALA L 301 " pdb=" CB ALA L 301 " both_signs ideal model delta sigma weight residual False 2.48 1.08 1.40 2.00e-01 2.50e+01 4.91e+01 ... (remaining 5558 not shown) Planarity restraints: 6621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP K 367 " 0.116 2.00e-02 2.50e+03 1.80e-01 3.25e+02 pdb=" C ASP K 367 " -0.306 2.00e-02 2.50e+03 pdb=" O ASP K 367 " 0.144 2.00e-02 2.50e+03 pdb=" N ARG K 369 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP P 367 " -0.116 2.00e-02 2.50e+03 1.80e-01 3.25e+02 pdb=" C ASP P 367 " 0.306 2.00e-02 2.50e+03 pdb=" O ASP P 367 " -0.144 2.00e-02 2.50e+03 pdb=" N ARG P 369 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP L 367 " 0.116 2.00e-02 2.50e+03 1.80e-01 3.25e+02 pdb=" C ASP L 367 " -0.306 2.00e-02 2.50e+03 pdb=" O ASP L 367 " 0.144 2.00e-02 2.50e+03 pdb=" N ARG L 369 " 0.047 2.00e-02 2.50e+03 ... (remaining 6618 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 2 1.91 - 2.65: 914 2.65 - 3.40: 49059 3.40 - 4.15: 95954 4.15 - 4.90: 167125 Nonbonded interactions: 313054 Sorted by model distance: nonbonded pdb=" CG2 THR H 27 " pdb=" OE1 GLN I 186 " model vdw 1.157 3.460 nonbonded pdb=" CG2 THR H 27 " pdb=" CD GLN I 186 " model vdw 1.851 3.690 nonbonded pdb=" N VAL P 298 " pdb=" O VAL P 298 " model vdw 2.148 2.496 nonbonded pdb=" OG SER D 367 " pdb=" NH2 ARG E 76 " model vdw 2.272 3.120 nonbonded pdb=" CB THR H 27 " pdb=" OE1 GLN I 186 " model vdw 2.272 3.470 ... (remaining 313049 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 19 through 60 or resid 76 through 173 or resid 178 through \ 408 or resid 410 through 458)) selection = (chain 'B' and (resid 19 through 60 or resid 76 through 173 or resid 178 through \ 226 or resid 229 through 329 or resid 335 through 408 or resid 410 through 442 \ or resid 449 through 458)) selection = (chain 'C' and (resid 19 through 60 or resid 76 through 173 or resid 178 through \ 226 or resid 229 through 408 or resid 410 through 442 or resid 449 through 458) \ ) selection = (chain 'D' and (resid 19 through 60 or resid 76 through 173 or resid 178 through \ 226 or resid 229 through 442 or resid 449 through 458)) selection = (chain 'E' and (resid 19 through 60 or resid 76 through 173 or resid 178 through \ 408 or resid 410 through 458)) selection = (chain 'F' and (resid 19 through 60 or resid 76 through 173 or resid 178 through \ 226 or resid 229 through 329 or resid 335 through 408 or resid 410 through 442 \ or resid 449 through 458)) selection = (chain 'G' and (resid 19 through 60 or resid 76 through 173 or resid 178 through \ 226 or resid 229 through 408 or resid 410 through 442 or resid 449 through 458) \ ) selection = (chain 'H' and (resid 19 through 60 or resid 76 through 173 or resid 178 through \ 226 or resid 229 through 442 or resid 449 through 458)) } ncs_group { reference = (chain 'J' 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 'K' 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 'L' 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 'M' 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)) selection = (chain 'N' 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)) selection = (chain 'O' 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)) selection = (chain 'P' 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 'Q' 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: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.130 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.440 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5049 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 : 0.024 1.520 37446 Z= 1.508 Angle : 1.714 28.947 50736 Z= 1.181 Chirality : 0.106 1.495 5561 Planarity : 0.010 0.180 6621 Dihedral : 15.324 89.795 13659 Min Nonbonded Distance : 1.157 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.06 % Favored : 97.57 % Rotamer: Outliers : 9.56 % Allowed : 5.31 % Favored : 85.13 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.12), residues: 4611 helix: 0.61 (0.12), residues: 1747 sheet: 0.23 (0.16), residues: 830 loop : -0.21 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 282 TYR 0.081 0.008 TYR G 236 PHE 0.030 0.006 PHE H 253 TRP 0.038 0.005 TRP F 448 HIS 0.014 0.003 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.02404 (37444) covalent geometry : angle 1.71379 (50732) SS BOND : bond 0.00037 ( 2) SS BOND : angle 3.24962 ( 4) hydrogen bonds : bond 0.14661 ( 1578) hydrogen bonds : angle 7.36752 ( 4422) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9222 Ramachandran restraints generated. 4611 Oldfield, 0 Emsley, 4611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 364 poor density : 587 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7063 (m-30) cc_final: 0.6854 (m-30) REVERT: A 104 LEU cc_start: 0.6045 (mt) cc_final: 0.5718 (tp) REVERT: A 125 LYS cc_start: 0.6110 (pttt) cc_final: 0.5628 (mmtt) REVERT: A 127 ILE cc_start: 0.6729 (mt) cc_final: 0.6199 (pt) REVERT: A 133 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7029 (mm-30) REVERT: A 153 GLN cc_start: 0.6555 (mp10) cc_final: 0.6349 (mm-40) REVERT: A 245 GLU cc_start: 0.6070 (mp0) cc_final: 0.5848 (pm20) REVERT: A 263 MET cc_start: 0.8487 (ptm) cc_final: 0.8184 (ptm) REVERT: A 294 MET cc_start: 0.7271 (ttt) cc_final: 0.6906 (ttp) REVERT: A 299 ASP cc_start: 0.7684 (p0) cc_final: 0.7246 (p0) REVERT: A 348 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6753 (mm-30) REVERT: A 350 HIS cc_start: 0.6746 (t-90) cc_final: 0.6331 (t70) REVERT: A 352 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6748 (mm-30) REVERT: A 354 ASP cc_start: 0.6179 (t0) cc_final: 0.5777 (t0) REVERT: A 382 TRP cc_start: 0.3947 (t-100) cc_final: 0.3563 (t-100) REVERT: A 418 ARG cc_start: 0.5309 (tpt-90) cc_final: 0.4896 (tpt-90) REVERT: B 23 THR cc_start: 0.5950 (m) cc_final: 0.5681 (p) REVERT: B 40 SER cc_start: 0.6068 (t) cc_final: 0.5591 (p) REVERT: B 77 TYR cc_start: 0.7065 (m-80) cc_final: 0.6848 (m-80) REVERT: B 78 LYS cc_start: 0.5971 (pttt) cc_final: 0.5752 (pttp) REVERT: B 94 TYR cc_start: 0.6822 (m-80) cc_final: 0.6599 (m-80) REVERT: B 128 ARG cc_start: 0.6432 (mtp180) cc_final: 0.5926 (mtp85) REVERT: B 169 CYS cc_start: 0.6179 (t) cc_final: 0.5706 (m) REVERT: B 195 ASP cc_start: 0.6218 (m-30) cc_final: 0.5976 (m-30) REVERT: B 206 GLN cc_start: 0.6370 (mt0) cc_final: 0.6142 (mp10) REVERT: B 223 HIS cc_start: 0.5863 (m-70) cc_final: 0.5514 (m90) REVERT: B 231 GLU cc_start: 0.4954 (pt0) cc_final: 0.4699 (pt0) REVERT: B 279 LYS cc_start: 0.6219 (tptp) cc_final: 0.5884 (mttm) REVERT: C 112 ASN cc_start: 0.7482 (t0) cc_final: 0.7183 (t0) REVERT: C 125 LYS cc_start: 0.6490 (pttt) cc_final: 0.5803 (mmtt) REVERT: C 133 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7022 (mm-30) REVERT: C 162 TYR cc_start: 0.6607 (m-80) cc_final: 0.6352 (m-80) REVERT: C 180 LYS cc_start: 0.5666 (OUTLIER) cc_final: 0.5433 (tttp) REVERT: C 184 ARG cc_start: 0.4420 (mtt90) cc_final: 0.4122 (ttm110) REVERT: C 249 LYS cc_start: 0.5943 (mttt) cc_final: 0.5520 (mtpt) REVERT: C 348 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6465 (mm-30) REVERT: C 383 HIS cc_start: 0.5885 (m-70) cc_final: 0.5653 (m170) REVERT: C 384 MET cc_start: 0.6252 (tpp) cc_final: 0.6034 (tpp) REVERT: C 418 ARG cc_start: 0.5411 (tpt-90) cc_final: 0.5168 (tpt-90) REVERT: D 40 SER cc_start: 0.6526 (t) cc_final: 0.6165 (p) REVERT: D 78 LYS cc_start: 0.5695 (pttt) cc_final: 0.5011 (ptpp) REVERT: D 80 LYS cc_start: 0.4847 (mttt) cc_final: 0.4550 (mtpt) REVERT: D 103 ASP cc_start: 0.7118 (m-30) cc_final: 0.6840 (m-30) REVERT: D 128 ARG cc_start: 0.6161 (mtp180) cc_final: 0.5373 (mtp85) REVERT: D 169 CYS cc_start: 0.7129 (p) cc_final: 0.6227 (m) REVERT: D 195 ASP cc_start: 0.6507 (m-30) cc_final: 0.5990 (m-30) REVERT: D 236 TYR cc_start: 0.7272 (m-80) cc_final: 0.6598 (m-80) REVERT: D 279 LYS cc_start: 0.6061 (tptp) cc_final: 0.5738 (mtpp) REVERT: D 302 ARG cc_start: 0.6732 (ptm-80) cc_final: 0.6297 (ttt180) REVERT: D 357 ARG cc_start: 0.5504 (mtp180) cc_final: 0.5289 (ttp80) REVERT: E 127 ILE cc_start: 0.6273 (mt) cc_final: 0.5832 (pt) REVERT: E 167 LEU cc_start: 0.6901 (mt) cc_final: 0.6688 (mt) REVERT: E 169 CYS cc_start: 0.6526 (p) cc_final: 0.6130 (t) REVERT: E 184 ARG cc_start: 0.4752 (mtt180) cc_final: 0.4407 (ttm110) REVERT: E 348 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6257 (mm-30) REVERT: E 352 GLU cc_start: 0.7431 (mm-30) cc_final: 0.5936 (tm-30) REVERT: F 57 GLU cc_start: 0.5218 (mm-30) cc_final: 0.4851 (mt-10) REVERT: F 77 TYR cc_start: 0.6907 (m-80) cc_final: 0.6612 (m-80) REVERT: F 78 LYS cc_start: 0.5416 (pttt) cc_final: 0.4471 (ptpp) REVERT: F 80 LYS cc_start: 0.5397 (mttt) cc_final: 0.5169 (mtpt) REVERT: F 128 ARG cc_start: 0.6053 (mtp180) cc_final: 0.5261 (mtp-110) REVERT: F 169 CYS cc_start: 0.6137 (t) cc_final: 0.5338 (m) REVERT: F 236 TYR cc_start: 0.7133 (m-80) cc_final: 0.6858 (m-80) REVERT: F 263 MET cc_start: 0.7885 (ptm) cc_final: 0.7604 (ptt) REVERT: F 279 LYS cc_start: 0.6306 (tptp) cc_final: 0.5982 (ttmm) REVERT: G 57 GLU cc_start: 0.5349 (mm-30) cc_final: 0.5115 (mm-30) REVERT: G 104 LEU cc_start: 0.5755 (mt) cc_final: 0.5497 (tp) REVERT: G 133 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6890 (mm-30) REVERT: G 169 CYS cc_start: 0.6758 (p) cc_final: 0.5691 (t) REVERT: G 206 GLN cc_start: 0.7248 (mp10) cc_final: 0.6923 (mp-120) REVERT: G 225 SER cc_start: 0.6223 (m) cc_final: 0.5883 (p) REVERT: G 252 GLU cc_start: 0.5949 (mm-30) cc_final: 0.5687 (mm-30) REVERT: G 302 ARG cc_start: 0.6562 (ptt90) cc_final: 0.6211 (mpt180) REVERT: G 340 LEU cc_start: 0.5311 (mt) cc_final: 0.5057 (mt) REVERT: G 344 ASP cc_start: 0.6419 (m-30) cc_final: 0.6113 (m-30) REVERT: G 348 GLU cc_start: 0.6728 (mm-30) cc_final: 0.6404 (mm-30) REVERT: G 352 GLU cc_start: 0.5906 (mt-10) cc_final: 0.5646 (tm-30) REVERT: G 354 ASP cc_start: 0.5829 (t0) cc_final: 0.5533 (t70) REVERT: G 356 SER cc_start: 0.7105 (p) cc_final: 0.6796 (p) REVERT: G 433 ASP cc_start: 0.4895 (t0) cc_final: 0.4429 (t70) REVERT: H 30 ASP cc_start: 0.6703 (m-30) cc_final: 0.6497 (t0) REVERT: H 40 SER cc_start: 0.6199 (t) cc_final: 0.5627 (p) REVERT: H 128 ARG cc_start: 0.6172 (mtp180) cc_final: 0.5573 (mtp85) REVERT: H 169 CYS cc_start: 0.6587 (p) cc_final: 0.6119 (m) REVERT: H 195 ASP cc_start: 0.6470 (m-30) cc_final: 0.6248 (m-30) REVERT: H 223 HIS cc_start: 0.5837 (m-70) cc_final: 0.5517 (m90) REVERT: H 228 GLU cc_start: 0.5679 (tt0) cc_final: 0.5258 (mt-10) REVERT: H 279 LYS cc_start: 0.6146 (tptp) cc_final: 0.5766 (ttmm) REVERT: I 59 GLU cc_start: 0.1628 (OUTLIER) cc_final: 0.1078 (tt0) REVERT: J 343 ARG cc_start: 0.1854 (OUTLIER) cc_final: 0.1600 (ttt180) REVERT: K 342 LYS cc_start: 0.1352 (OUTLIER) cc_final: 0.0784 (mmtt) REVERT: K 347 LEU cc_start: -0.0997 (OUTLIER) cc_final: -0.1255 (mm) REVERT: K 393 GLU cc_start: 0.0864 (OUTLIER) cc_final: 0.0141 (pp20) REVERT: L 302 THR cc_start: 0.0068 (OUTLIER) cc_final: -0.0327 (p) REVERT: M 347 LEU cc_start: 0.0261 (OUTLIER) cc_final: -0.0632 (pp) REVERT: M 435 ARG cc_start: 0.0120 (OUTLIER) cc_final: -0.0288 (mtt90) REVERT: N 306 VAL cc_start: 0.0639 (OUTLIER) cc_final: 0.0388 (t) REVERT: N 389 ARG cc_start: 0.1001 (OUTLIER) cc_final: 0.0471 (mmt-90) REVERT: N 435 ARG cc_start: -0.0156 (OUTLIER) cc_final: -0.0398 (ptt-90) REVERT: O 342 LYS cc_start: 0.1139 (OUTLIER) cc_final: -0.0185 (mmmt) REVERT: P 292 ARG cc_start: 0.1436 (OUTLIER) cc_final: 0.0868 (mtp180) REVERT: Q 306 VAL cc_start: -0.0327 (OUTLIER) cc_final: -0.0582 (p) outliers start: 364 outliers final: 176 residues processed: 947 average time/residue: 0.2678 time to fit residues: 392.7451 Evaluate side-chains 563 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 372 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 LYS Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 136 ARG Chi-restraints excluded: chain I residue 179 GLN Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain J residue 288 ILE Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 291 VAL Chi-restraints excluded: chain J residue 294 LYS Chi-restraints excluded: chain J residue 295 PHE Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 316 GLU Chi-restraints excluded: chain J residue 318 LYS Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 333 LYS Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 342 LYS Chi-restraints excluded: chain J residue 343 ARG Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 361 VAL Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain J residue 393 GLU Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 418 ARG Chi-restraints excluded: chain J residue 420 VAL Chi-restraints excluded: chain J residue 435 ARG Chi-restraints excluded: chain K residue 292 ARG Chi-restraints excluded: chain K residue 294 LYS Chi-restraints excluded: chain K residue 295 PHE Chi-restraints excluded: chain K residue 298 VAL Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 333 LYS Chi-restraints excluded: chain K residue 335 VAL Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain K residue 343 ARG Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 366 ARG Chi-restraints excluded: chain K residue 370 LYS Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 393 GLU Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 401 VAL Chi-restraints excluded: chain K residue 402 VAL Chi-restraints excluded: chain K residue 413 SER Chi-restraints excluded: chain K residue 418 ARG Chi-restraints excluded: chain K residue 435 ARG Chi-restraints excluded: chain L residue 288 ILE Chi-restraints excluded: chain L residue 292 ARG Chi-restraints excluded: chain L residue 294 LYS Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 302 THR Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 311 LYS Chi-restraints excluded: chain L residue 314 GLU Chi-restraints excluded: chain L residue 316 GLU Chi-restraints excluded: chain L residue 319 ILE Chi-restraints excluded: chain L residue 333 LYS Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain L residue 347 LEU Chi-restraints excluded: chain L residue 361 VAL Chi-restraints excluded: chain L residue 366 ARG Chi-restraints excluded: chain L residue 370 LYS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 388 VAL Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 393 GLU Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain L residue 405 ASN Chi-restraints excluded: chain L residue 408 LYS Chi-restraints excluded: chain L residue 413 SER Chi-restraints excluded: chain L residue 418 ARG Chi-restraints excluded: chain L residue 420 VAL Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain L residue 435 ARG Chi-restraints excluded: chain M residue 288 ILE Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 313 GLU Chi-restraints excluded: chain M residue 317 LYS Chi-restraints excluded: chain M residue 318 LYS Chi-restraints excluded: chain M residue 324 MET Chi-restraints excluded: chain M residue 331 ASP Chi-restraints excluded: chain M residue 332 PHE Chi-restraints excluded: chain M residue 335 VAL Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 343 ARG Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 364 SER Chi-restraints excluded: chain M residue 369 ARG Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 375 ASP Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 387 ARG Chi-restraints excluded: chain M residue 424 LEU Chi-restraints excluded: chain M residue 435 ARG Chi-restraints excluded: chain N residue 288 ILE Chi-restraints excluded: chain N residue 304 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 317 LYS Chi-restraints excluded: chain N residue 318 LYS Chi-restraints excluded: chain N residue 332 PHE Chi-restraints excluded: chain N residue 342 LYS Chi-restraints excluded: chain N residue 343 ARG Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain N residue 361 VAL Chi-restraints excluded: chain N residue 364 SER Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 389 ARG Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 402 VAL Chi-restraints excluded: chain N residue 424 LEU Chi-restraints excluded: chain N residue 435 ARG Chi-restraints excluded: chain O residue 304 VAL Chi-restraints excluded: chain O residue 317 LYS Chi-restraints excluded: chain O residue 318 LYS Chi-restraints excluded: chain O residue 324 MET Chi-restraints excluded: chain O residue 331 ASP Chi-restraints excluded: chain O residue 332 PHE Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 342 LYS Chi-restraints excluded: chain O residue 364 SER Chi-restraints excluded: chain O residue 371 VAL Chi-restraints excluded: chain O residue 375 ASP Chi-restraints excluded: chain O residue 387 ARG Chi-restraints excluded: chain O residue 389 ARG Chi-restraints excluded: chain O residue 391 VAL Chi-restraints excluded: chain O residue 393 GLU Chi-restraints excluded: chain O residue 396 ASP Chi-restraints excluded: chain O residue 401 VAL Chi-restraints excluded: chain O residue 424 LEU Chi-restraints excluded: chain O residue 435 ARG Chi-restraints excluded: chain P residue 288 ILE Chi-restraints excluded: chain P residue 292 ARG Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 298 VAL Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 311 LYS Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 333 LYS Chi-restraints excluded: chain P residue 342 LYS Chi-restraints excluded: chain P residue 343 ARG Chi-restraints excluded: chain P residue 364 SER Chi-restraints excluded: chain P residue 366 ARG Chi-restraints excluded: chain P residue 370 LYS Chi-restraints excluded: chain P residue 371 VAL Chi-restraints excluded: chain P residue 391 VAL Chi-restraints excluded: chain P residue 393 GLU Chi-restraints excluded: chain P residue 401 VAL Chi-restraints excluded: chain P residue 418 ARG Chi-restraints excluded: chain P residue 420 VAL Chi-restraints excluded: chain P residue 430 VAL Chi-restraints excluded: chain P residue 431 VAL Chi-restraints excluded: chain P residue 435 ARG Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 300 GLU Chi-restraints excluded: chain Q residue 305 VAL Chi-restraints excluded: chain Q residue 306 VAL Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 316 GLU Chi-restraints excluded: chain Q residue 317 LYS Chi-restraints excluded: chain Q residue 318 LYS Chi-restraints excluded: chain Q residue 324 MET Chi-restraints excluded: chain Q residue 332 PHE Chi-restraints excluded: chain Q residue 335 VAL Chi-restraints excluded: chain Q residue 342 LYS Chi-restraints excluded: chain Q residue 361 VAL Chi-restraints excluded: chain Q residue 369 ARG Chi-restraints excluded: chain Q residue 375 ASP Chi-restraints excluded: chain Q residue 382 LEU Chi-restraints excluded: chain Q residue 387 ARG Chi-restraints excluded: chain Q residue 389 ARG Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 393 GLU Chi-restraints excluded: chain Q residue 402 VAL Chi-restraints excluded: chain Q residue 424 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 50.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 398 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS B 350 HIS C 350 HIS D 83 HIS D 204 ASN E 146 GLN E 350 HIS E 398 GLN F 92 ASN F 146 GLN F 264 HIS F 350 HIS G 146 GLN G 350 HIS H 350 HIS I 77 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.240594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.229256 restraints weight = 38518.265| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 0.46 r_work: 0.4271 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.4220 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 37446 Z= 0.160 Angle : 0.657 14.253 50736 Z= 0.357 Chirality : 0.046 0.230 5561 Planarity : 0.006 0.088 6621 Dihedral : 10.540 59.775 5558 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.91 % Favored : 97.79 % Rotamer: Outliers : 5.31 % Allowed : 10.46 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.12), residues: 4619 helix: 1.47 (0.12), residues: 1758 sheet: 0.38 (0.17), residues: 770 loop : -0.28 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 366 TYR 0.019 0.002 TYR E 236 PHE 0.024 0.002 PHE E 342 TRP 0.012 0.001 TRP L 341 HIS 0.007 0.001 HIS I 87 Details of bonding type rmsd covalent geometry : bond 0.00351 (37444) covalent geometry : angle 0.65627 (50732) SS BOND : bond 0.00780 ( 2) SS BOND : angle 3.40978 ( 4) hydrogen bonds : bond 0.04496 ( 1578) hydrogen bonds : angle 5.43117 ( 4422) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 407 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.3649 (ppp) cc_final: 0.1934 (mpp) REVERT: A 127 ILE cc_start: 0.8639 (mt) cc_final: 0.8284 (pt) REVERT: A 418 ARG cc_start: 0.6691 (tpt-90) cc_final: 0.6230 (tpt-90) REVERT: C 166 MET cc_start: 0.8142 (mtm) cc_final: 0.7935 (mpp) REVERT: C 228 GLU cc_start: 0.5769 (tt0) cc_final: 0.5466 (mt-10) REVERT: C 249 LYS cc_start: 0.8199 (mttt) cc_final: 0.7948 (mtpt) REVERT: C 352 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: D 78 LYS cc_start: 0.7075 (pttt) cc_final: 0.6487 (ptpp) REVERT: D 195 ASP cc_start: 0.6939 (m-30) cc_final: 0.6651 (m-30) REVERT: E 352 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7735 (tm-30) REVERT: F 78 LYS cc_start: 0.6734 (pttt) cc_final: 0.6350 (ptpp) REVERT: F 399 PHE cc_start: 0.7725 (m-80) cc_final: 0.7490 (m-80) REVERT: G 299 ASP cc_start: 0.7787 (p0) cc_final: 0.7551 (p0) REVERT: H 399 PHE cc_start: 0.7855 (m-80) cc_final: 0.7629 (m-80) REVERT: I 59 GLU cc_start: 0.2862 (OUTLIER) cc_final: 0.2505 (tm-30) REVERT: K 311 LYS cc_start: 0.0220 (OUTLIER) cc_final: -0.0145 (mmtp) REVERT: K 342 LYS cc_start: 0.1920 (OUTLIER) cc_final: 0.0764 (mptt) REVERT: K 343 ARG cc_start: -0.0051 (OUTLIER) cc_final: -0.0352 (mtp85) REVERT: K 393 GLU cc_start: 0.2265 (OUTLIER) cc_final: 0.1091 (pp20) REVERT: L 324 MET cc_start: 0.1206 (mmm) cc_final: -0.0092 (pmm) REVERT: L 370 LYS cc_start: -0.0011 (OUTLIER) cc_final: -0.0643 (mmtm) REVERT: L 426 MET cc_start: 0.1562 (ttt) cc_final: 0.1241 (tpp) REVERT: O 342 LYS cc_start: 0.2687 (OUTLIER) cc_final: 0.0872 (mmmt) REVERT: P 297 GLU cc_start: 0.2037 (OUTLIER) cc_final: 0.0581 (pm20) REVERT: Q 300 GLU cc_start: 0.0816 (OUTLIER) cc_final: -0.0257 (pm20) outliers start: 202 outliers final: 107 residues processed: 598 average time/residue: 0.2801 time to fit residues: 258.8425 Evaluate side-chains 447 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 330 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 136 ARG Chi-restraints excluded: chain I residue 175 ASN Chi-restraints excluded: chain I residue 179 GLN Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain J residue 294 LYS Chi-restraints excluded: chain J residue 303 SER Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 391 VAL Chi-restraints excluded: chain J residue 393 GLU Chi-restraints excluded: chain J residue 418 ARG Chi-restraints excluded: chain K residue 292 ARG Chi-restraints excluded: chain K residue 294 LYS Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 335 VAL Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain K residue 343 ARG Chi-restraints excluded: chain K residue 370 LYS Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 393 GLU Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 418 ARG Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 435 ARG Chi-restraints excluded: chain L residue 292 ARG Chi-restraints excluded: chain L residue 294 LYS Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 316 GLU Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 366 ARG Chi-restraints excluded: chain L residue 370 LYS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 388 VAL Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 393 GLU Chi-restraints excluded: chain L residue 418 ARG Chi-restraints excluded: chain L residue 420 VAL Chi-restraints excluded: chain L residue 422 GLU Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain M residue 288 ILE Chi-restraints excluded: chain M residue 303 SER Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 313 GLU Chi-restraints excluded: chain M residue 317 LYS Chi-restraints excluded: chain M residue 331 ASP Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 343 ARG Chi-restraints excluded: chain M residue 369 ARG Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 375 ASP Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 387 ARG Chi-restraints excluded: chain M residue 424 LEU Chi-restraints excluded: chain N residue 303 SER Chi-restraints excluded: chain N residue 304 VAL Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 402 VAL Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain O residue 317 LYS Chi-restraints excluded: chain O residue 331 ASP Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 342 LYS Chi-restraints excluded: chain O residue 371 VAL Chi-restraints excluded: chain O residue 387 ARG Chi-restraints excluded: chain O residue 391 VAL Chi-restraints excluded: chain O residue 393 GLU Chi-restraints excluded: chain O residue 401 VAL Chi-restraints excluded: chain O residue 435 ARG Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain P residue 333 LYS Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 343 ARG Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain P residue 371 VAL Chi-restraints excluded: chain P residue 393 GLU Chi-restraints excluded: chain P residue 401 VAL Chi-restraints excluded: chain P residue 418 ARG Chi-restraints excluded: chain P residue 430 VAL Chi-restraints excluded: chain P residue 431 VAL Chi-restraints excluded: chain Q residue 300 GLU Chi-restraints excluded: chain Q residue 305 VAL Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 332 PHE Chi-restraints excluded: chain Q residue 335 VAL Chi-restraints excluded: chain Q residue 369 ARG Chi-restraints excluded: chain Q residue 382 LEU Chi-restraints excluded: chain Q residue 387 ARG Chi-restraints excluded: chain Q residue 424 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 456 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 418 optimal weight: 0.9990 chunk 317 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN D 209 GLN D 383 HIS E 383 HIS F 146 GLN F 204 ASN G 146 GLN G 383 HIS G 398 GLN H 204 ASN I 113 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.235335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.224012 restraints weight = 38314.934| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 0.46 r_work: 0.4235 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.4190 rms_B_bonded: 1.60 restraints_weight: 0.2500 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 37446 Z= 0.185 Angle : 0.643 10.715 50736 Z= 0.340 Chirality : 0.047 0.209 5561 Planarity : 0.005 0.091 6621 Dihedral : 8.377 58.401 5309 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.62 % Favored : 97.16 % Rotamer: Outliers : 4.20 % Allowed : 13.08 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.09 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: 0.49 (0.12), residues: 4619 helix: 1.36 (0.12), residues: 1754 sheet: 0.31 (0.17), residues: 758 loop : -0.50 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 347 TYR 0.026 0.002 TYR E 236 PHE 0.030 0.003 PHE E 342 TRP 0.020 0.002 TRP J 341 HIS 0.006 0.001 HIS F 264 Details of bonding type rmsd covalent geometry : bond 0.00439 (37444) covalent geometry : angle 0.64245 (50732) SS BOND : bond 0.00776 ( 2) SS BOND : angle 3.27241 ( 4) hydrogen bonds : bond 0.04413 ( 1578) hydrogen bonds : angle 5.21845 ( 4422) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 386 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.3725 (ppp) cc_final: 0.2078 (mmp) REVERT: A 127 ILE cc_start: 0.8575 (mt) cc_final: 0.8048 (pt) REVERT: A 128 ARG cc_start: 0.7135 (ttp80) cc_final: 0.6932 (ttm170) REVERT: A 352 GLU cc_start: 0.7938 (tp30) cc_final: 0.7610 (mm-30) REVERT: A 418 ARG cc_start: 0.6858 (tpt-90) cc_final: 0.6496 (tpt170) REVERT: B 443 ARG cc_start: 0.5021 (OUTLIER) cc_final: 0.4512 (ttm110) REVERT: C 29 LYS cc_start: 0.7603 (mttt) cc_final: 0.7313 (mtmm) REVERT: D 201 GLU cc_start: 0.6677 (pm20) cc_final: 0.6368 (pm20) REVERT: E 259 MET cc_start: 0.8268 (mmm) cc_final: 0.7999 (mmm) REVERT: E 283 ASP cc_start: 0.7474 (m-30) cc_final: 0.7227 (m-30) REVERT: E 344 ASP cc_start: 0.7601 (m-30) cc_final: 0.7340 (m-30) REVERT: F 78 LYS cc_start: 0.6989 (pttt) cc_final: 0.6504 (ptpp) REVERT: F 201 GLU cc_start: 0.7011 (pp20) cc_final: 0.6780 (pp20) REVERT: G 352 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: H 78 LYS cc_start: 0.7072 (pttt) cc_final: 0.6426 (ptpp) REVERT: I 59 GLU cc_start: 0.3250 (OUTLIER) cc_final: 0.2733 (tm-30) REVERT: K 316 GLU cc_start: 0.0318 (OUTLIER) cc_final: 0.0043 (pp20) REVERT: K 393 GLU cc_start: 0.2281 (OUTLIER) cc_final: 0.1879 (pt0) REVERT: M 327 ILE cc_start: 0.0003 (OUTLIER) cc_final: -0.0452 (mp) REVERT: M 424 LEU cc_start: 0.2340 (OUTLIER) cc_final: 0.1898 (tp) REVERT: N 313 GLU cc_start: 0.0512 (OUTLIER) cc_final: -0.0494 (tm-30) REVERT: O 317 LYS cc_start: 0.0950 (OUTLIER) cc_final: 0.0522 (ptmt) REVERT: O 342 LYS cc_start: 0.2760 (OUTLIER) cc_final: 0.1243 (mtpp) REVERT: O 426 MET cc_start: 0.0236 (ttt) cc_final: -0.0051 (ttt) REVERT: P 295 PHE cc_start: 0.2607 (OUTLIER) cc_final: 0.2096 (m-10) REVERT: P 297 GLU cc_start: 0.2254 (OUTLIER) cc_final: 0.0911 (pm20) REVERT: P 324 MET cc_start: 0.3114 (mtt) cc_final: 0.2892 (mtt) REVERT: P 338 GLU cc_start: 0.1169 (OUTLIER) cc_final: -0.0224 (pm20) outliers start: 160 outliers final: 109 residues processed: 537 average time/residue: 0.2734 time to fit residues: 229.7483 Evaluate side-chains 455 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 333 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 356 SER Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 390 ILE Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 179 GLN Chi-restraints excluded: chain J residue 288 ILE Chi-restraints excluded: chain J residue 294 LYS Chi-restraints excluded: chain J residue 333 LYS Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 343 ARG Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 393 GLU Chi-restraints excluded: chain J residue 418 ARG Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 292 ARG Chi-restraints excluded: chain K residue 311 LYS Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 335 VAL Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain K residue 370 LYS Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 374 TRP Chi-restraints excluded: chain K residue 393 GLU Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 418 ARG Chi-restraints excluded: chain K residue 428 VAL Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 435 ARG Chi-restraints excluded: chain L residue 292 ARG Chi-restraints excluded: chain L residue 294 LYS Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 319 ILE Chi-restraints excluded: chain L residue 333 LYS Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 370 LYS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 418 ARG Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain M residue 288 ILE Chi-restraints excluded: chain M residue 303 SER Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 313 GLU Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 387 ARG Chi-restraints excluded: chain M residue 424 LEU Chi-restraints excluded: chain N residue 303 SER Chi-restraints excluded: chain N residue 304 VAL Chi-restraints excluded: chain N residue 313 GLU Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain O residue 317 LYS Chi-restraints excluded: chain O residue 324 MET Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 342 LYS Chi-restraints excluded: chain O residue 353 VAL Chi-restraints excluded: chain O residue 371 VAL Chi-restraints excluded: chain O residue 387 ARG Chi-restraints excluded: chain O residue 391 VAL Chi-restraints excluded: chain O residue 393 GLU Chi-restraints excluded: chain O residue 401 VAL Chi-restraints excluded: chain O residue 405 ASN Chi-restraints excluded: chain P residue 295 PHE Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 345 VAL Chi-restraints excluded: chain P residue 356 ILE Chi-restraints excluded: chain P residue 371 VAL Chi-restraints excluded: chain P residue 401 VAL Chi-restraints excluded: chain P residue 418 ARG Chi-restraints excluded: chain P residue 431 VAL Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 316 GLU Chi-restraints excluded: chain Q residue 332 PHE Chi-restraints excluded: chain Q residue 369 ARG Chi-restraints excluded: chain Q residue 382 LEU Chi-restraints excluded: chain Q residue 387 ARG Chi-restraints excluded: chain Q residue 424 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 19 optimal weight: 9.9990 chunk 267 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 455 optimal weight: 0.0970 chunk 282 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 372 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 123 optimal weight: 0.0570 chunk 7 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 overall best weight: 3.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN C 112 ASN C 146 GLN ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN F 383 HIS G 112 ASN G 146 GLN G 202 ASN H 146 GLN ** H 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.232526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.210106 restraints weight = 37977.323| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 0.89 r_work: 0.3889 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.3761 rms_B_bonded: 3.04 restraints_weight: 0.1250 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 37446 Z= 0.195 Angle : 0.632 10.608 50736 Z= 0.330 Chirality : 0.047 0.198 5561 Planarity : 0.005 0.090 6621 Dihedral : 7.588 61.334 5237 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.62 % Favored : 97.19 % Rotamer: Outliers : 3.91 % Allowed : 14.27 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.12), residues: 4619 helix: 1.14 (0.12), residues: 1752 sheet: 0.21 (0.18), residues: 708 loop : -0.56 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 38 TYR 0.021 0.002 TYR E 236 PHE 0.032 0.002 PHE O 332 TRP 0.014 0.002 TRP J 344 HIS 0.006 0.002 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00475 (37444) covalent geometry : angle 0.63116 (50732) SS BOND : bond 0.00825 ( 2) SS BOND : angle 3.27309 ( 4) hydrogen bonds : bond 0.04343 ( 1578) hydrogen bonds : angle 5.16453 ( 4422) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 363 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASN cc_start: 0.8741 (t0) cc_final: 0.8532 (t0) REVERT: A 127 ILE cc_start: 0.8639 (mt) cc_final: 0.8074 (pt) REVERT: A 128 ARG cc_start: 0.7448 (ttp80) cc_final: 0.7224 (ttp80) REVERT: A 352 GLU cc_start: 0.8201 (tp30) cc_final: 0.7977 (mm-30) REVERT: A 418 ARG cc_start: 0.7095 (tpt-90) cc_final: 0.6772 (tpt170) REVERT: A 451 GLU cc_start: 0.6280 (mp0) cc_final: 0.6051 (mp0) REVERT: B 103 ASP cc_start: 0.7923 (m-30) cc_final: 0.7680 (m-30) REVERT: B 200 ASP cc_start: 0.6127 (t0) cc_final: 0.5668 (t0) REVERT: B 443 ARG cc_start: 0.4860 (OUTLIER) cc_final: 0.4371 (ttm110) REVERT: C 451 GLU cc_start: 0.6109 (mp0) cc_final: 0.5821 (mp0) REVERT: E 103 ASP cc_start: 0.7667 (m-30) cc_final: 0.7441 (m-30) REVERT: E 112 ASN cc_start: 0.8742 (t0) cc_final: 0.8485 (t0) REVERT: E 283 ASP cc_start: 0.7652 (m-30) cc_final: 0.7381 (m-30) REVERT: E 302 ARG cc_start: 0.7466 (ttp80) cc_final: 0.7008 (tpt90) REVERT: E 344 ASP cc_start: 0.8033 (m-30) cc_final: 0.7581 (m-30) REVERT: F 78 LYS cc_start: 0.7246 (pttt) cc_final: 0.6589 (ptpp) REVERT: F 201 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6350 (pp20) REVERT: G 344 ASP cc_start: 0.8161 (m-30) cc_final: 0.7807 (m-30) REVERT: H 300 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.6563 (tpt-90) REVERT: I 59 GLU cc_start: 0.2997 (OUTLIER) cc_final: 0.2257 (tm-30) REVERT: K 292 ARG cc_start: 0.0752 (OUTLIER) cc_final: 0.0472 (mtp180) REVERT: K 333 LYS cc_start: 0.1951 (OUTLIER) cc_final: 0.0979 (ttpt) REVERT: K 393 GLU cc_start: 0.2044 (OUTLIER) cc_final: 0.1703 (pt0) REVERT: L 370 LYS cc_start: 0.0344 (OUTLIER) cc_final: 0.0046 (mmtm) REVERT: M 327 ILE cc_start: -0.0237 (OUTLIER) cc_final: -0.0549 (mp) REVERT: M 342 LYS cc_start: 0.0922 (OUTLIER) cc_final: 0.0676 (mptp) REVERT: N 313 GLU cc_start: 0.0497 (OUTLIER) cc_final: -0.0576 (tm-30) REVERT: O 317 LYS cc_start: 0.0530 (OUTLIER) cc_final: 0.0064 (ptmt) REVERT: O 342 LYS cc_start: 0.2390 (OUTLIER) cc_final: 0.0715 (mtpp) REVERT: O 426 MET cc_start: -0.0073 (ttt) cc_final: -0.0383 (ttt) REVERT: P 295 PHE cc_start: 0.3221 (OUTLIER) cc_final: 0.2575 (m-10) REVERT: P 338 GLU cc_start: 0.0913 (OUTLIER) cc_final: -0.0450 (pm20) REVERT: Q 313 GLU cc_start: -0.1698 (OUTLIER) cc_final: -0.2771 (tm-30) outliers start: 149 outliers final: 100 residues processed: 494 average time/residue: 0.2651 time to fit residues: 206.0237 Evaluate side-chains 454 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 338 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 356 SER Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 390 ILE Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 300 ARG Chi-restraints excluded: chain H residue 325 SER Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain J residue 288 ILE Chi-restraints excluded: chain J residue 294 LYS Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 418 ARG Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain K residue 292 ARG Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 333 LYS Chi-restraints excluded: chain K residue 335 VAL Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 393 GLU Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 418 ARG Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 435 ARG Chi-restraints excluded: chain L residue 294 LYS Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 319 ILE Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 356 ILE Chi-restraints excluded: chain L residue 366 ARG Chi-restraints excluded: chain L residue 370 LYS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 418 ARG Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain M residue 288 ILE Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 303 SER Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 313 GLU Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 387 ARG Chi-restraints excluded: chain N residue 303 SER Chi-restraints excluded: chain N residue 304 VAL Chi-restraints excluded: chain N residue 305 VAL Chi-restraints excluded: chain N residue 313 GLU Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 382 LEU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 426 MET Chi-restraints excluded: chain O residue 317 LYS Chi-restraints excluded: chain O residue 324 MET Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 342 LYS Chi-restraints excluded: chain O residue 353 VAL Chi-restraints excluded: chain O residue 371 VAL Chi-restraints excluded: chain O residue 387 ARG Chi-restraints excluded: chain O residue 393 GLU Chi-restraints excluded: chain O residue 405 ASN Chi-restraints excluded: chain P residue 295 PHE Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 345 VAL Chi-restraints excluded: chain P residue 371 VAL Chi-restraints excluded: chain P residue 418 ARG Chi-restraints excluded: chain P residue 431 VAL Chi-restraints excluded: chain Q residue 298 VAL Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 324 MET Chi-restraints excluded: chain Q residue 332 PHE Chi-restraints excluded: chain Q residue 361 VAL Chi-restraints excluded: chain Q residue 369 ARG Chi-restraints excluded: chain Q residue 382 LEU Chi-restraints excluded: chain Q residue 387 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 393 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 406 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 398 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 460 optimal weight: 50.0000 chunk 221 optimal weight: 6.9990 chunk 392 optimal weight: 9.9990 chunk 354 optimal weight: 8.9990 chunk 311 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 206 GLN A 264 HIS ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS C 112 ASN C 146 GLN C 264 HIS C 426 GLN ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN E 264 HIS ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 GLN F 146 GLN G 112 ASN G 146 GLN G 202 ASN G 264 HIS G 398 GLN G 426 GLN H 380 HIS H 383 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.230271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.207526 restraints weight = 37833.102| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 0.90 r_work: 0.3844 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.3697 rms_B_bonded: 3.23 restraints_weight: 0.1250 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 37446 Z= 0.249 Angle : 0.690 11.386 50736 Z= 0.359 Chirality : 0.049 0.227 5561 Planarity : 0.006 0.089 6621 Dihedral : 7.237 59.541 5204 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.20 % Favored : 96.60 % Rotamer: Outliers : 4.47 % Allowed : 14.84 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.09 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -0.15 (0.12), residues: 4619 helix: 0.71 (0.12), residues: 1753 sheet: -0.01 (0.18), residues: 736 loop : -0.74 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 282 TYR 0.025 0.002 TYR I 41 PHE 0.033 0.003 PHE O 332 TRP 0.013 0.002 TRP O 374 HIS 0.009 0.002 HIS G 380 Details of bonding type rmsd covalent geometry : bond 0.00617 (37444) covalent geometry : angle 0.68897 (50732) SS BOND : bond 0.00758 ( 2) SS BOND : angle 3.65954 ( 4) hydrogen bonds : bond 0.04866 ( 1578) hydrogen bonds : angle 5.32147 ( 4422) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 351 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.7974 (tt) REVERT: A 112 ASN cc_start: 0.8791 (t0) cc_final: 0.8558 (t0) REVERT: A 128 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7275 (ttm170) REVERT: B 200 ASP cc_start: 0.6205 (t0) cc_final: 0.5711 (t0) REVERT: B 201 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6423 (pp20) REVERT: B 443 ARG cc_start: 0.4910 (OUTLIER) cc_final: 0.4519 (ttm110) REVERT: C 352 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: E 112 ASN cc_start: 0.8820 (t0) cc_final: 0.8549 (t0) REVERT: E 283 ASP cc_start: 0.7722 (m-30) cc_final: 0.7446 (m-30) REVERT: E 344 ASP cc_start: 0.8167 (m-30) cc_final: 0.7705 (m-30) REVERT: E 352 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: F 48 ASP cc_start: 0.7439 (m-30) cc_final: 0.7212 (m-30) REVERT: F 78 LYS cc_start: 0.7300 (pttt) cc_final: 0.6667 (ptpp) REVERT: F 201 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6385 (pp20) REVERT: G 344 ASP cc_start: 0.8194 (m-30) cc_final: 0.7878 (m-30) REVERT: G 352 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: I 59 GLU cc_start: 0.3031 (OUTLIER) cc_final: 0.2293 (tm-30) REVERT: J 288 ILE cc_start: 0.3261 (OUTLIER) cc_final: 0.2536 (mp) REVERT: K 333 LYS cc_start: 0.2048 (OUTLIER) cc_final: 0.1005 (ttpt) REVERT: K 342 LYS cc_start: 0.1366 (OUTLIER) cc_final: -0.0344 (tptp) REVERT: K 393 GLU cc_start: 0.1950 (OUTLIER) cc_final: 0.1635 (pt0) REVERT: L 324 MET cc_start: 0.1861 (mmm) cc_final: -0.0195 (pmm) REVERT: L 418 ARG cc_start: 0.0814 (OUTLIER) cc_final: 0.0608 (mmt90) REVERT: M 327 ILE cc_start: -0.0167 (OUTLIER) cc_final: -0.0505 (mp) REVERT: M 342 LYS cc_start: 0.0913 (OUTLIER) cc_final: 0.0654 (mptp) REVERT: M 387 ARG cc_start: 0.1265 (OUTLIER) cc_final: -0.0813 (mmt-90) REVERT: M 426 MET cc_start: 0.1128 (OUTLIER) cc_final: 0.0237 (ttp) REVERT: N 313 GLU cc_start: 0.0484 (OUTLIER) cc_final: 0.0075 (tt0) REVERT: O 317 LYS cc_start: 0.0549 (OUTLIER) cc_final: -0.0254 (ptmt) REVERT: O 342 LYS cc_start: 0.2265 (OUTLIER) cc_final: 0.0593 (mtpp) REVERT: O 426 MET cc_start: -0.0129 (ttt) cc_final: -0.0462 (ttt) REVERT: P 338 GLU cc_start: 0.0948 (OUTLIER) cc_final: -0.0429 (pm20) outliers start: 170 outliers final: 113 residues processed: 500 average time/residue: 0.2650 time to fit residues: 208.0410 Evaluate side-chains 471 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 337 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 356 SER Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 390 ILE Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 325 SER Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 395 SER Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain J residue 288 ILE Chi-restraints excluded: chain J residue 294 LYS Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 361 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 418 ARG Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain K residue 292 ARG Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 333 LYS Chi-restraints excluded: chain K residue 335 VAL Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 393 GLU Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain K residue 435 ARG Chi-restraints excluded: chain L residue 294 LYS Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 319 ILE Chi-restraints excluded: chain L residue 347 LEU Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 418 ARG Chi-restraints excluded: chain L residue 420 VAL Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain M residue 288 ILE Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 303 SER Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 313 GLU Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 342 LYS Chi-restraints excluded: chain M residue 363 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 387 ARG Chi-restraints excluded: chain M residue 424 LEU Chi-restraints excluded: chain M residue 426 MET Chi-restraints excluded: chain N residue 303 SER Chi-restraints excluded: chain N residue 304 VAL Chi-restraints excluded: chain N residue 305 VAL Chi-restraints excluded: chain N residue 313 GLU Chi-restraints excluded: chain N residue 319 ILE Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 426 MET Chi-restraints excluded: chain O residue 317 LYS Chi-restraints excluded: chain O residue 324 MET Chi-restraints excluded: chain O residue 332 PHE Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 342 LYS Chi-restraints excluded: chain O residue 353 VAL Chi-restraints excluded: chain O residue 387 ARG Chi-restraints excluded: chain O residue 393 GLU Chi-restraints excluded: chain O residue 401 VAL Chi-restraints excluded: chain O residue 405 ASN Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 345 VAL Chi-restraints excluded: chain P residue 353 VAL Chi-restraints excluded: chain P residue 356 ILE Chi-restraints excluded: chain P residue 371 VAL Chi-restraints excluded: chain P residue 402 VAL Chi-restraints excluded: chain P residue 418 ARG Chi-restraints excluded: chain P residue 431 VAL Chi-restraints excluded: chain Q residue 298 VAL Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 332 PHE Chi-restraints excluded: chain Q residue 361 VAL Chi-restraints excluded: chain Q residue 369 ARG Chi-restraints excluded: chain Q residue 382 LEU Chi-restraints excluded: chain Q residue 387 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 303 optimal weight: 0.8980 chunk 207 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 365 optimal weight: 0.0670 chunk 428 optimal weight: 5.9990 chunk 435 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 348 optimal weight: 20.0000 chunk 180 optimal weight: 0.6980 chunk 394 optimal weight: 4.9990 chunk 380 optimal weight: 7.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 202 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS C 112 ASN C 146 GLN C 202 ASN D 295 HIS D 350 HIS D 380 HIS E 146 GLN ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN G 146 GLN G 202 ASN H 295 HIS L 351 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.235616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.224639 restraints weight = 38201.508| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 0.44 r_work: 0.4231 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.4191 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 37446 Z= 0.108 Angle : 0.519 9.584 50736 Z= 0.275 Chirality : 0.043 0.235 5561 Planarity : 0.005 0.088 6621 Dihedral : 6.545 58.663 5187 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.29 % Favored : 97.60 % Rotamer: Outliers : 2.86 % Allowed : 16.53 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.12), residues: 4619 helix: 1.47 (0.13), residues: 1751 sheet: 0.08 (0.19), residues: 712 loop : -0.56 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 366 TYR 0.015 0.001 TYR I 41 PHE 0.029 0.002 PHE O 332 TRP 0.014 0.001 TRP A 459 HIS 0.006 0.001 HIS H 150 Details of bonding type rmsd covalent geometry : bond 0.00243 (37444) covalent geometry : angle 0.51851 (50732) SS BOND : bond 0.01138 ( 2) SS BOND : angle 2.01388 ( 4) hydrogen bonds : bond 0.03272 ( 1578) hydrogen bonds : angle 4.85980 ( 4422) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 357 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.3580 (ppp) cc_final: 0.2004 (mmp) REVERT: A 104 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7887 (tt) REVERT: A 112 ASN cc_start: 0.8524 (t0) cc_final: 0.8303 (t0) REVERT: A 127 ILE cc_start: 0.8482 (mt) cc_final: 0.8003 (pt) REVERT: A 128 ARG cc_start: 0.7097 (ttp80) cc_final: 0.6851 (ttm170) REVERT: A 352 GLU cc_start: 0.7742 (tp30) cc_final: 0.7530 (mm-30) REVERT: B 200 ASP cc_start: 0.5885 (t0) cc_final: 0.5463 (t0) REVERT: B 201 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6343 (pp20) REVERT: B 443 ARG cc_start: 0.5051 (OUTLIER) cc_final: 0.4698 (ttm110) REVERT: C 77 TYR cc_start: 0.7667 (m-10) cc_final: 0.7436 (m-80) REVERT: C 352 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: E 259 MET cc_start: 0.8125 (mmm) cc_final: 0.7916 (mmm) REVERT: E 344 ASP cc_start: 0.7569 (m-30) cc_final: 0.7275 (m-30) REVERT: E 352 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: F 78 LYS cc_start: 0.6905 (pttt) cc_final: 0.6342 (ptpp) REVERT: F 201 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6213 (pp20) REVERT: F 380 HIS cc_start: 0.5404 (OUTLIER) cc_final: 0.4302 (p90) REVERT: G 344 ASP cc_start: 0.7546 (m-30) cc_final: 0.7316 (m-30) REVERT: G 352 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: G 357 ARG cc_start: 0.8314 (mtp180) cc_final: 0.8114 (mtp85) REVERT: H 300 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6772 (tpt-90) REVERT: I 59 GLU cc_start: 0.3197 (OUTLIER) cc_final: 0.2599 (tm-30) REVERT: J 288 ILE cc_start: 0.3200 (OUTLIER) cc_final: 0.2624 (mp) REVERT: K 342 LYS cc_start: 0.1337 (OUTLIER) cc_final: 0.0380 (mptp) REVERT: L 324 MET cc_start: 0.1808 (mmm) cc_final: -0.0083 (pmm) REVERT: L 374 TRP cc_start: -0.1456 (OUTLIER) cc_final: -0.2875 (p90) REVERT: L 418 ARG cc_start: 0.0840 (OUTLIER) cc_final: 0.0628 (mmt90) REVERT: M 426 MET cc_start: 0.1279 (OUTLIER) cc_final: -0.0158 (ttm) REVERT: N 313 GLU cc_start: 0.0882 (OUTLIER) cc_final: 0.0283 (tt0) REVERT: N 426 MET cc_start: -0.0229 (OUTLIER) cc_final: -0.1116 (ttp) REVERT: O 342 LYS cc_start: 0.2547 (OUTLIER) cc_final: 0.0997 (mtpp) REVERT: O 426 MET cc_start: 0.0147 (ttt) cc_final: -0.0287 (ttt) REVERT: P 338 GLU cc_start: 0.1211 (OUTLIER) cc_final: -0.0195 (pm20) REVERT: P 370 LYS cc_start: -0.0684 (OUTLIER) cc_final: -0.1051 (tmtm) outliers start: 109 outliers final: 65 residues processed: 446 average time/residue: 0.2696 time to fit residues: 187.0575 Evaluate side-chains 409 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 324 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain H residue 300 ARG Chi-restraints excluded: chain H residue 395 SER Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain J residue 288 ILE Chi-restraints excluded: chain J residue 294 LYS Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 361 VAL Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain K residue 292 ARG Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 383 VAL Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 435 ARG Chi-restraints excluded: chain L residue 294 LYS Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 333 LYS Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 374 TRP Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 418 ARG Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain M residue 288 ILE Chi-restraints excluded: chain M residue 303 SER Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 313 GLU Chi-restraints excluded: chain M residue 363 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 382 LEU Chi-restraints excluded: chain M residue 387 ARG Chi-restraints excluded: chain M residue 424 LEU Chi-restraints excluded: chain M residue 426 MET Chi-restraints excluded: chain N residue 303 SER Chi-restraints excluded: chain N residue 304 VAL Chi-restraints excluded: chain N residue 305 VAL Chi-restraints excluded: chain N residue 313 GLU Chi-restraints excluded: chain N residue 333 LYS Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 426 MET Chi-restraints excluded: chain O residue 317 LYS Chi-restraints excluded: chain O residue 324 MET Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 342 LYS Chi-restraints excluded: chain O residue 353 VAL Chi-restraints excluded: chain O residue 387 ARG Chi-restraints excluded: chain O residue 393 GLU Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 370 LYS Chi-restraints excluded: chain P residue 431 VAL Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 332 PHE Chi-restraints excluded: chain Q residue 382 LEU Chi-restraints excluded: chain Q residue 387 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 79 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 408 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 461 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 460 optimal weight: 50.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS B 303 ASN C 112 ASN C 146 GLN D 303 ASN E 112 ASN E 146 GLN ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS F 146 GLN F 204 ASN F 303 ASN G 112 ASN G 146 GLN G 202 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.230907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.219738 restraints weight = 37875.265| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 0.46 r_work: 0.3825 rms_B_bonded: 0.70 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 37446 Z= 0.226 Angle : 0.653 10.494 50736 Z= 0.341 Chirality : 0.049 0.207 5561 Planarity : 0.006 0.094 6621 Dihedral : 6.399 59.114 5166 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.36 % Favored : 96.54 % Rotamer: Outliers : 3.26 % Allowed : 16.79 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.09 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -0.03 (0.12), residues: 4619 helix: 0.87 (0.12), residues: 1753 sheet: 0.04 (0.19), residues: 722 loop : -0.72 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 389 TYR 0.017 0.002 TYR I 41 PHE 0.029 0.003 PHE F 342 TRP 0.018 0.002 TRP A 459 HIS 0.007 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00559 (37444) covalent geometry : angle 0.65259 (50732) SS BOND : bond 0.00797 ( 2) SS BOND : angle 3.28435 ( 4) hydrogen bonds : bond 0.04603 ( 1578) hydrogen bonds : angle 5.19475 ( 4422) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 344 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.3072 (ppp) cc_final: 0.1561 (mmp) REVERT: A 104 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7893 (tt) REVERT: A 112 ASN cc_start: 0.8807 (t0) cc_final: 0.8576 (t0) REVERT: A 128 ARG cc_start: 0.7374 (ttp80) cc_final: 0.7122 (ttm170) REVERT: B 200 ASP cc_start: 0.6199 (t0) cc_final: 0.5720 (t0) REVERT: B 201 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6473 (pp20) REVERT: C 352 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: D 380 HIS cc_start: 0.5291 (OUTLIER) cc_final: 0.4342 (p90) REVERT: E 352 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: F 78 LYS cc_start: 0.7197 (pttt) cc_final: 0.6366 (ptpp) REVERT: F 201 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6321 (pp20) REVERT: F 380 HIS cc_start: 0.5348 (OUTLIER) cc_final: 0.4097 (p90) REVERT: G 344 ASP cc_start: 0.7932 (m-30) cc_final: 0.7513 (m-30) REVERT: G 352 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: H 155 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7548 (tt0) REVERT: H 201 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6273 (pp20) REVERT: H 300 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6736 (tpt-90) REVERT: H 380 HIS cc_start: 0.5327 (OUTLIER) cc_final: 0.4292 (p90) REVERT: I 59 GLU cc_start: 0.2145 (OUTLIER) cc_final: 0.1399 (tm-30) REVERT: L 324 MET cc_start: 0.2010 (mmm) cc_final: -0.0315 (pmm) REVERT: M 327 ILE cc_start: -0.0496 (OUTLIER) cc_final: -0.0893 (mt) REVERT: M 426 MET cc_start: 0.0725 (OUTLIER) cc_final: -0.0647 (ttm) REVERT: N 313 GLU cc_start: 0.0062 (OUTLIER) cc_final: -0.0241 (tt0) REVERT: O 342 LYS cc_start: 0.1737 (OUTLIER) cc_final: 0.0236 (mtpp) REVERT: O 426 MET cc_start: -0.0483 (ttt) cc_final: -0.0762 (ttt) REVERT: P 338 GLU cc_start: 0.0505 (OUTLIER) cc_final: -0.0715 (pm20) REVERT: P 370 LYS cc_start: -0.0756 (OUTLIER) cc_final: -0.1328 (tmtm) REVERT: Q 313 GLU cc_start: -0.1600 (OUTLIER) cc_final: -0.2738 (tm-30) outliers start: 124 outliers final: 83 residues processed: 443 average time/residue: 0.2724 time to fit residues: 187.6999 Evaluate side-chains 433 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 331 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 356 SER Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 390 ILE Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 300 ARG Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 395 SER Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain J residue 294 LYS Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 361 VAL Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain K residue 292 ARG Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 411 LYS Chi-restraints excluded: chain K residue 435 ARG Chi-restraints excluded: chain L residue 294 LYS Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain M residue 303 SER Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 313 GLU Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 363 VAL Chi-restraints excluded: chain M residue 364 SER Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 387 ARG Chi-restraints excluded: chain M residue 424 LEU Chi-restraints excluded: chain M residue 426 MET Chi-restraints excluded: chain N residue 303 SER Chi-restraints excluded: chain N residue 304 VAL Chi-restraints excluded: chain N residue 305 VAL Chi-restraints excluded: chain N residue 313 GLU Chi-restraints excluded: chain N residue 333 LYS Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 426 MET Chi-restraints excluded: chain O residue 317 LYS Chi-restraints excluded: chain O residue 324 MET Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 342 LYS Chi-restraints excluded: chain O residue 353 VAL Chi-restraints excluded: chain O residue 387 ARG Chi-restraints excluded: chain O residue 393 GLU Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 370 LYS Chi-restraints excluded: chain P residue 371 VAL Chi-restraints excluded: chain P residue 431 VAL Chi-restraints excluded: chain Q residue 298 VAL Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 332 PHE Chi-restraints excluded: chain Q residue 387 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 66 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 347 optimal weight: 0.0040 chunk 175 optimal weight: 0.6980 chunk 411 optimal weight: 10.0000 chunk 421 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 423 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 415 optimal weight: 50.0000 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 324 HIS A 383 HIS C 112 ASN C 146 GLN C 202 ASN D 303 ASN E 146 GLN ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN H 204 ASN H 307 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.234366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.207420 restraints weight = 37814.280| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 1.02 r_work: 0.3896 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work: 0.3724 rms_B_bonded: 3.92 restraints_weight: 0.1250 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 37446 Z= 0.119 Angle : 0.527 9.345 50736 Z= 0.279 Chirality : 0.044 0.175 5561 Planarity : 0.005 0.093 6621 Dihedral : 5.858 58.241 5155 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.47 % Favored : 97.47 % Rotamer: Outliers : 2.84 % Allowed : 17.42 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.12), residues: 4619 helix: 1.38 (0.12), residues: 1747 sheet: 0.03 (0.19), residues: 712 loop : -0.63 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 389 TYR 0.014 0.001 TYR I 41 PHE 0.022 0.002 PHE E 342 TRP 0.012 0.001 TRP A 459 HIS 0.006 0.001 HIS H 150 Details of bonding type rmsd covalent geometry : bond 0.00283 (37444) covalent geometry : angle 0.52635 (50732) SS BOND : bond 0.00878 ( 2) SS BOND : angle 2.25686 ( 4) hydrogen bonds : bond 0.03428 ( 1578) hydrogen bonds : angle 4.87326 ( 4422) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 332 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.3314 (ppp) cc_final: 0.1777 (mmp) REVERT: A 104 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8012 (tt) REVERT: A 112 ASN cc_start: 0.8766 (t0) cc_final: 0.8526 (t0) REVERT: B 200 ASP cc_start: 0.6190 (t0) cc_final: 0.5704 (t0) REVERT: B 201 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6416 (pp20) REVERT: B 340 LEU cc_start: 0.7815 (mt) cc_final: 0.7613 (mp) REVERT: C 77 TYR cc_start: 0.7858 (m-10) cc_final: 0.7611 (m-80) REVERT: C 124 PHE cc_start: 0.7562 (t80) cc_final: 0.7300 (t80) REVERT: C 352 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: D 380 HIS cc_start: 0.5420 (OUTLIER) cc_final: 0.4504 (p90) REVERT: E 259 MET cc_start: 0.8330 (mmm) cc_final: 0.8125 (mmm) REVERT: E 344 ASP cc_start: 0.8050 (m-30) cc_final: 0.7831 (m-30) REVERT: E 352 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: F 78 LYS cc_start: 0.7216 (pttt) cc_final: 0.6462 (ptpp) REVERT: F 201 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6348 (pp20) REVERT: F 380 HIS cc_start: 0.5494 (OUTLIER) cc_final: 0.4343 (p90) REVERT: G 344 ASP cc_start: 0.8138 (m-30) cc_final: 0.7820 (m-30) REVERT: G 352 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: H 201 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6320 (pp20) REVERT: H 300 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6942 (tpt-90) REVERT: I 59 GLU cc_start: 0.2803 (OUTLIER) cc_final: 0.2086 (tm-30) REVERT: J 288 ILE cc_start: 0.3445 (OUTLIER) cc_final: 0.2578 (mp) REVERT: J 319 ILE cc_start: -0.1420 (OUTLIER) cc_final: -0.1862 (mp) REVERT: K 411 LYS cc_start: -0.0842 (OUTLIER) cc_final: -0.1198 (tttm) REVERT: L 324 MET cc_start: 0.1849 (mmm) cc_final: -0.0199 (pmm) REVERT: M 288 ILE cc_start: 0.0359 (OUTLIER) cc_final: 0.0136 (pt) REVERT: M 387 ARG cc_start: 0.1303 (OUTLIER) cc_final: -0.1218 (mmt-90) REVERT: M 426 MET cc_start: 0.0857 (OUTLIER) cc_final: -0.0430 (ttm) REVERT: N 313 GLU cc_start: 0.0580 (OUTLIER) cc_final: 0.0057 (tt0) REVERT: N 426 MET cc_start: -0.0135 (OUTLIER) cc_final: -0.0889 (ttp) REVERT: O 342 LYS cc_start: 0.2209 (OUTLIER) cc_final: 0.0655 (mtpp) REVERT: O 393 GLU cc_start: 0.0870 (OUTLIER) cc_final: 0.0405 (pp20) REVERT: O 426 MET cc_start: -0.0187 (ttt) cc_final: -0.0550 (ttt) REVERT: P 338 GLU cc_start: 0.0942 (OUTLIER) cc_final: -0.0462 (pm20) REVERT: P 370 LYS cc_start: -0.0824 (OUTLIER) cc_final: -0.1306 (mmtm) outliers start: 108 outliers final: 65 residues processed: 421 average time/residue: 0.2675 time to fit residues: 174.9986 Evaluate side-chains 409 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 321 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 300 ARG Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 395 SER Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain J residue 288 ILE Chi-restraints excluded: chain J residue 294 LYS Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 361 VAL Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 411 LYS Chi-restraints excluded: chain K residue 418 ARG Chi-restraints excluded: chain K residue 435 ARG Chi-restraints excluded: chain L residue 294 LYS Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain M residue 288 ILE Chi-restraints excluded: chain M residue 303 SER Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 313 GLU Chi-restraints excluded: chain M residue 363 VAL Chi-restraints excluded: chain M residue 364 SER Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 387 ARG Chi-restraints excluded: chain M residue 424 LEU Chi-restraints excluded: chain M residue 426 MET Chi-restraints excluded: chain N residue 303 SER Chi-restraints excluded: chain N residue 304 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 313 GLU Chi-restraints excluded: chain N residue 333 LYS Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 426 MET Chi-restraints excluded: chain O residue 317 LYS Chi-restraints excluded: chain O residue 324 MET Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 342 LYS Chi-restraints excluded: chain O residue 353 VAL Chi-restraints excluded: chain O residue 387 ARG Chi-restraints excluded: chain O residue 393 GLU Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 370 LYS Chi-restraints excluded: chain P residue 431 VAL Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 332 PHE Chi-restraints excluded: chain Q residue 387 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 5 optimal weight: 1.9990 chunk 454 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 275 optimal weight: 8.9990 chunk 333 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 430 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS B 206 GLN C 112 ASN C 146 GLN D 264 HIS D 303 ASN ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS F 146 GLN G 112 ASN G 146 GLN H 264 HIS H 303 ASN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.229363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.206466 restraints weight = 37918.418| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 0.89 r_work: 0.3846 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.3696 rms_B_bonded: 3.33 restraints_weight: 0.1250 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 37446 Z= 0.257 Angle : 0.662 10.283 50736 Z= 0.347 Chirality : 0.050 0.205 5561 Planarity : 0.006 0.092 6621 Dihedral : 6.072 58.654 5150 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 3.13 % Allowed : 17.29 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.09 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -0.12 (0.12), residues: 4619 helix: 0.81 (0.12), residues: 1753 sheet: -0.09 (0.19), residues: 740 loop : -0.76 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 136 TYR 0.018 0.002 TYR I 41 PHE 0.029 0.003 PHE A 399 TRP 0.020 0.002 TRP A 459 HIS 0.006 0.001 HIS F 264 Details of bonding type rmsd covalent geometry : bond 0.00638 (37444) covalent geometry : angle 0.66124 (50732) SS BOND : bond 0.00637 ( 2) SS BOND : angle 3.44462 ( 4) hydrogen bonds : bond 0.04723 ( 1578) hydrogen bonds : angle 5.22105 ( 4422) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 344 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.3274 (ppp) cc_final: 0.1767 (mmp) REVERT: A 104 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8049 (tt) REVERT: A 112 ASN cc_start: 0.8824 (t0) cc_final: 0.8617 (t0) REVERT: B 166 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6898 (mtt) REVERT: B 201 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6518 (pp20) REVERT: C 124 PHE cc_start: 0.7585 (t80) cc_final: 0.7302 (t80) REVERT: C 352 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: D 155 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7705 (tt0) REVERT: D 380 HIS cc_start: 0.5410 (OUTLIER) cc_final: 0.4423 (p90) REVERT: E 344 ASP cc_start: 0.8187 (m-30) cc_final: 0.7845 (m-30) REVERT: E 352 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: F 201 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6415 (pp20) REVERT: F 380 HIS cc_start: 0.5476 (OUTLIER) cc_final: 0.4299 (p90) REVERT: G 104 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.7965 (tt) REVERT: G 344 ASP cc_start: 0.8241 (m-30) cc_final: 0.7837 (m-30) REVERT: G 352 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: H 155 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7674 (tt0) REVERT: H 201 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6357 (pp20) REVERT: H 300 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.6972 (tpt-90) REVERT: H 380 HIS cc_start: 0.5539 (OUTLIER) cc_final: 0.4594 (p90) REVERT: I 59 GLU cc_start: 0.2878 (OUTLIER) cc_final: 0.2165 (tm-30) REVERT: J 319 ILE cc_start: -0.1441 (OUTLIER) cc_final: -0.1853 (mt) REVERT: K 347 LEU cc_start: 0.0426 (OUTLIER) cc_final: 0.0200 (mm) REVERT: K 426 MET cc_start: 0.2124 (pmm) cc_final: 0.1438 (tpp) REVERT: L 324 MET cc_start: 0.1938 (mmm) cc_final: -0.0189 (pmm) REVERT: M 288 ILE cc_start: 0.0608 (OUTLIER) cc_final: 0.0400 (pt) REVERT: M 426 MET cc_start: 0.0932 (OUTLIER) cc_final: -0.0403 (ttm) REVERT: N 313 GLU cc_start: 0.0624 (OUTLIER) cc_final: 0.0098 (tt0) REVERT: N 426 MET cc_start: 0.0100 (OUTLIER) cc_final: -0.0844 (ttp) REVERT: O 342 LYS cc_start: 0.2328 (OUTLIER) cc_final: 0.0611 (mtpp) REVERT: P 338 GLU cc_start: 0.1060 (OUTLIER) cc_final: -0.0429 (pm20) REVERT: P 370 LYS cc_start: -0.0781 (OUTLIER) cc_final: -0.1156 (tmtm) REVERT: Q 313 GLU cc_start: -0.1762 (OUTLIER) cc_final: -0.2565 (tm-30) outliers start: 119 outliers final: 83 residues processed: 438 average time/residue: 0.2721 time to fit residues: 185.7399 Evaluate side-chains 442 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 335 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 356 SER Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 390 ILE Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 300 ARG Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 395 SER Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain J residue 294 LYS Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 411 LYS Chi-restraints excluded: chain K residue 435 ARG Chi-restraints excluded: chain L residue 294 LYS Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 420 VAL Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain M residue 288 ILE Chi-restraints excluded: chain M residue 303 SER Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 313 GLU Chi-restraints excluded: chain M residue 363 VAL Chi-restraints excluded: chain M residue 364 SER Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 387 ARG Chi-restraints excluded: chain M residue 426 MET Chi-restraints excluded: chain N residue 303 SER Chi-restraints excluded: chain N residue 304 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 313 GLU Chi-restraints excluded: chain N residue 333 LYS Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 426 MET Chi-restraints excluded: chain O residue 317 LYS Chi-restraints excluded: chain O residue 324 MET Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 342 LYS Chi-restraints excluded: chain O residue 353 VAL Chi-restraints excluded: chain O residue 387 ARG Chi-restraints excluded: chain O residue 393 GLU Chi-restraints excluded: chain O residue 401 VAL Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 370 LYS Chi-restraints excluded: chain P residue 431 VAL Chi-restraints excluded: chain Q residue 298 VAL Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 332 PHE Chi-restraints excluded: chain Q residue 387 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 180 optimal weight: 0.5980 chunk 397 optimal weight: 7.9990 chunk 220 optimal weight: 0.9980 chunk 410 optimal weight: 30.0000 chunk 412 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 257 optimal weight: 0.7980 chunk 273 optimal weight: 10.0000 chunk 429 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 202 ASN A 206 GLN A 324 HIS A 383 HIS ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN D 307 HIS E 146 GLN E 202 ASN ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN H 303 ASN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.234316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.223220 restraints weight = 37885.270| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 0.44 r_work: 0.3903 rms_B_bonded: 0.68 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 1.15 restraints_weight: 0.2500 r_work: 0.3589 rms_B_bonded: 2.15 restraints_weight: 0.1250 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 37446 Z= 0.119 Angle : 0.537 9.146 50736 Z= 0.285 Chirality : 0.044 0.177 5561 Planarity : 0.005 0.092 6621 Dihedral : 5.755 59.396 5149 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 2.50 % Allowed : 17.92 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.09 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: 0.23 (0.12), residues: 4619 helix: 1.30 (0.12), residues: 1747 sheet: -0.02 (0.19), residues: 712 loop : -0.71 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 389 TYR 0.017 0.001 TYR B 94 PHE 0.021 0.002 PHE E 342 TRP 0.017 0.001 TRP F 408 HIS 0.007 0.001 HIS H 150 Details of bonding type rmsd covalent geometry : bond 0.00284 (37444) covalent geometry : angle 0.53661 (50732) SS BOND : bond 0.00906 ( 2) SS BOND : angle 2.11701 ( 4) hydrogen bonds : bond 0.03515 ( 1578) hydrogen bonds : angle 4.92313 ( 4422) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9238 Ramachandran restraints generated. 4619 Oldfield, 0 Emsley, 4619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 338 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.2977 (ppp) cc_final: 0.1527 (mmp) REVERT: A 104 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.7958 (tt) REVERT: A 112 ASN cc_start: 0.8729 (t0) cc_final: 0.8507 (t0) REVERT: A 357 ARG cc_start: 0.8362 (mtp-110) cc_final: 0.8159 (mtp85) REVERT: A 384 MET cc_start: 0.7256 (mtp) cc_final: 0.7017 (mtp) REVERT: B 201 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6418 (pp20) REVERT: C 77 TYR cc_start: 0.7734 (m-10) cc_final: 0.7504 (m-80) REVERT: C 124 PHE cc_start: 0.7543 (t80) cc_final: 0.7259 (t80) REVERT: C 166 MET cc_start: 0.8455 (mtm) cc_final: 0.8232 (mpp) REVERT: C 352 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: D 380 HIS cc_start: 0.5375 (OUTLIER) cc_final: 0.4383 (p90) REVERT: E 344 ASP cc_start: 0.7864 (m-30) cc_final: 0.7612 (m-30) REVERT: E 352 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: F 78 LYS cc_start: 0.7365 (pttm) cc_final: 0.6294 (ptpp) REVERT: F 201 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6355 (pp20) REVERT: F 380 HIS cc_start: 0.5436 (OUTLIER) cc_final: 0.4224 (p90) REVERT: G 104 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7801 (tt) REVERT: G 344 ASP cc_start: 0.7843 (m-30) cc_final: 0.7480 (m-30) REVERT: G 352 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: H 155 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7641 (tt0) REVERT: H 201 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6224 (pp20) REVERT: H 300 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6886 (tpt-90) REVERT: H 380 HIS cc_start: 0.5450 (OUTLIER) cc_final: 0.4420 (p90) REVERT: I 59 GLU cc_start: 0.2431 (OUTLIER) cc_final: 0.1707 (tm-30) REVERT: J 319 ILE cc_start: -0.1512 (OUTLIER) cc_final: -0.1896 (mt) REVERT: K 426 MET cc_start: 0.2097 (pmm) cc_final: 0.1396 (tpp) REVERT: L 324 MET cc_start: 0.2008 (mmm) cc_final: -0.0249 (pmm) REVERT: M 387 ARG cc_start: 0.1564 (OUTLIER) cc_final: -0.1110 (mmt-90) REVERT: M 426 MET cc_start: 0.0769 (OUTLIER) cc_final: -0.0662 (ttm) REVERT: N 313 GLU cc_start: 0.0308 (OUTLIER) cc_final: -0.0137 (tt0) REVERT: N 426 MET cc_start: -0.0237 (OUTLIER) cc_final: -0.1050 (ttp) REVERT: O 342 LYS cc_start: 0.2042 (OUTLIER) cc_final: 0.0514 (mtpp) REVERT: O 393 GLU cc_start: 0.0586 (OUTLIER) cc_final: 0.0213 (pp20) REVERT: P 338 GLU cc_start: 0.0691 (OUTLIER) cc_final: -0.0649 (pm20) REVERT: P 370 LYS cc_start: -0.0786 (OUTLIER) cc_final: -0.1034 (mmtm) REVERT: P 429 LEU cc_start: -0.1644 (OUTLIER) cc_final: -0.1883 (tp) REVERT: Q 313 GLU cc_start: -0.1730 (OUTLIER) cc_final: -0.2571 (tm-30) outliers start: 95 outliers final: 60 residues processed: 414 average time/residue: 0.2770 time to fit residues: 176.7714 Evaluate side-chains 417 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 333 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 380 HIS Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain H residue 300 ARG Chi-restraints excluded: chain H residue 338 SER Chi-restraints excluded: chain H residue 380 HIS Chi-restraints excluded: chain H residue 395 SER Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain J residue 294 LYS Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain K residue 316 GLU Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain K residue 396 ASP Chi-restraints excluded: chain K residue 411 LYS Chi-restraints excluded: chain K residue 435 ARG Chi-restraints excluded: chain L residue 294 LYS Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain M residue 303 SER Chi-restraints excluded: chain M residue 304 VAL Chi-restraints excluded: chain M residue 313 GLU Chi-restraints excluded: chain M residue 363 VAL Chi-restraints excluded: chain M residue 364 SER Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 387 ARG Chi-restraints excluded: chain M residue 426 MET Chi-restraints excluded: chain N residue 303 SER Chi-restraints excluded: chain N residue 304 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 313 GLU Chi-restraints excluded: chain N residue 333 LYS Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 426 MET Chi-restraints excluded: chain O residue 317 LYS Chi-restraints excluded: chain O residue 324 MET Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 342 LYS Chi-restraints excluded: chain O residue 353 VAL Chi-restraints excluded: chain O residue 387 ARG Chi-restraints excluded: chain O residue 393 GLU Chi-restraints excluded: chain P residue 305 VAL Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 370 LYS Chi-restraints excluded: chain P residue 429 LEU Chi-restraints excluded: chain P residue 431 VAL Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 332 PHE Chi-restraints excluded: chain Q residue 387 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 256 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 441 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 274 optimal weight: 2.9990 chunk 343 optimal weight: 30.0000 chunk 408 optimal weight: 9.9990 chunk 430 optimal weight: 40.0000 chunk 375 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 324 HIS A 383 HIS C 112 ASN C 146 GLN C 202 ASN E 146 GLN ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS F 146 GLN G 112 ASN G 146 GLN H 303 ASN ** I 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.228151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.153507 restraints weight = 37682.847| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 6.03 r_work: 0.2901 rms_B_bonded: 5.85 restraints_weight: 2.0000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 37446 Z= 0.255 Angle : 0.676 10.512 50736 Z= 0.354 Chirality : 0.050 0.210 5561 Planarity : 0.006 0.091 6621 Dihedral : 6.081 59.880 5149 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.96 % Favored : 95.97 % Rotamer: Outliers : 2.79 % Allowed : 17.74 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.09 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -0.24 (0.12), residues: 4619 helix: 0.70 (0.12), residues: 1753 sheet: -0.08 (0.19), residues: 736 loop : -0.85 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 389 TYR 0.018 0.002 TYR I 41 PHE 0.029 0.003 PHE A 342 TRP 0.022 0.002 TRP F 408 HIS 0.007 0.001 HIS F 264 Details of bonding type rmsd covalent geometry : bond 0.00644 (37444) covalent geometry : angle 0.67505 (50732) SS BOND : bond 0.00748 ( 2) SS BOND : angle 3.45694 ( 4) hydrogen bonds : bond 0.04799 ( 1578) hydrogen bonds : angle 5.27121 ( 4422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12321.19 seconds wall clock time: 210 minutes 27.65 seconds (12627.65 seconds total)