Starting phenix.real_space_refine on Sat Feb 7 08:55:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ixi_60970/02_2026/9ixi_60970_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ixi_60970/02_2026/9ixi_60970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ixi_60970/02_2026/9ixi_60970_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ixi_60970/02_2026/9ixi_60970_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ixi_60970/02_2026/9ixi_60970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ixi_60970/02_2026/9ixi_60970.map" } resolution = 3.01 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= 0.002 sd= 0.035 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 240 5.16 5 C 19636 2.51 5 N 5396 2.21 5 O 5848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31120 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3325 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "B" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3325 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "C" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3325 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "D" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3325 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "E" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3299 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 389} Chain: "F" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3299 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 389} Chain: "G" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3299 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 389} Chain: "H" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3299 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 389} Chain: "I" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1156 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "J" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1156 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "K" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1156 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "L" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1156 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Time building chain proxies: 7.43, per 1000 atoms: 0.24 Number of scatterers: 31120 At special positions: 0 Unit cell: (188.24, 185.12, 195.52, 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 240 16.00 O 5848 8.00 N 5396 7.00 C 19636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.05 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.12 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.02 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.02 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.02 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.02 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.07 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 78 " distance=2.06 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.06 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.02 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.20 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 78 " distance=2.09 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.02 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.02 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.02 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.02 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.25 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.04 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 271 " distance=2.02 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.03 Simple disulfide: pdb=" SG CYS D 306 " - pdb=" SG CYS D 380 " distance=2.03 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 370 " distance=2.09 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 125 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 28 " distance=2.02 Simple disulfide: pdb=" SG CYS E 91 " - pdb=" SG CYS E 105 " distance=2.03 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 266 " distance=2.04 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 203 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 125 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 28 " distance=2.02 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 105 " distance=2.03 Simple disulfide: pdb=" SG CYS F 153 " - pdb=" SG CYS F 266 " distance=2.04 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 225 " distance=2.13 Simple disulfide: pdb=" SG CYS F 203 " - pdb=" SG CYS F 220 " distance=2.04 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 125 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 28 " distance=2.02 Simple disulfide: pdb=" SG CYS G 91 " - pdb=" SG CYS G 105 " distance=2.02 Simple disulfide: pdb=" SG CYS G 153 " - pdb=" SG CYS G 266 " distance=2.02 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 225 " distance=2.26 Simple disulfide: pdb=" SG CYS G 203 " - pdb=" SG CYS G 220 " distance=2.02 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 125 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 28 " distance=2.02 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 266 " distance=2.03 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 225 " distance=2.23 Simple disulfide: pdb=" SG CYS H 203 " - pdb=" SG CYS H 220 " distance=2.07 Simple disulfide: pdb=" SG CYS I 113 " - pdb=" SG CYS I 128 " 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: 2.83 Conformation dependent library (CDL) restraints added in 1.6 seconds 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7520 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 75 sheets defined 14.2% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.506A pdb=" N LYS A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 407 through 438 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 256 through 259 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 407 through 438 removed outlier: 3.566A pdb=" N GLN B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 407 through 436 removed outlier: 3.661A pdb=" N GLN C 411 " --> pdb=" O MET C 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 256 through 259 Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 398 through 403 removed outlier: 3.985A pdb=" N SER D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 406 No H-bonds generated for 'chain 'D' and resid 404 through 406' Processing helix chain 'D' and resid 407 through 436 Processing helix chain 'E' and resid 4 through 10 removed outlier: 3.827A pdb=" N VAL E 8 " --> pdb=" O ASN E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 351 through 363 Processing helix chain 'E' and resid 365 through 402 Proline residue: E 399 - end of helix Processing helix chain 'E' and resid 409 through 417 Processing helix chain 'F' and resid 4 through 10 removed outlier: 3.750A pdb=" N VAL F 8 " --> pdb=" O ASN F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 60 No H-bonds generated for 'chain 'F' and resid 58 through 60' Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 351 through 363 Processing helix chain 'F' and resid 363 through 396 removed outlier: 3.661A pdb=" N VAL F 368 " --> pdb=" O PRO F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 403 Processing helix chain 'F' and resid 409 through 416 Processing helix chain 'G' and resid 5 through 10 removed outlier: 4.207A pdb=" N VAL G 8 " --> pdb=" O ASN G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 83 No H-bonds generated for 'chain 'G' and resid 81 through 83' Processing helix chain 'G' and resid 221 through 223 No H-bonds generated for 'chain 'G' and resid 221 through 223' Processing helix chain 'G' and resid 351 through 363 Processing helix chain 'G' and resid 365 through 403 Proline residue: G 399 - end of helix Processing helix chain 'G' and resid 409 through 416 Processing helix chain 'H' and resid 81 through 83 No H-bonds generated for 'chain 'H' and resid 81 through 83' Processing helix chain 'H' and resid 178 through 181 Processing helix chain 'H' and resid 221 through 225 Processing helix chain 'H' and resid 351 through 363 Processing helix chain 'H' and resid 365 through 402 Proline residue: H 399 - end of helix Processing helix chain 'H' and resid 409 through 416 Processing helix chain 'I' and resid 146 through 151 Processing helix chain 'I' and resid 168 through 175 removed outlier: 4.869A pdb=" N SER I 173 " --> pdb=" O HIS I 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 175 removed outlier: 5.132A pdb=" N SER J 173 " --> pdb=" O HIS J 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 151 Processing helix chain 'L' and resid 146 through 151 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 19 removed outlier: 3.623A pdb=" N GLU A 30 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS A 132 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL A 36 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER A 130 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU A 38 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N SER A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU A 42 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA A 124 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR A 46 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N SER A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR A 48 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N PHE A 118 " --> pdb=" O THR A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 140 through 147 current: chain 'A' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 183 through 186 current: chain 'A' and resid 213 through 215 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 213 through 215 current: chain 'A' and resid 267 through 269 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 54 current: chain 'A' and resid 101 through 110 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA6, first strand: chain 'A' and resid 296 through 305 removed outlier: 5.472A pdb=" N ASP A 298 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA A 321 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL A 315 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 8 Processing sheet with id=AB1, first strand: chain 'B' and resid 14 through 19 removed outlier: 3.687A pdb=" N GLU B 30 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS B 132 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 36 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER B 130 " --> pdb=" O VAL B 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 140 through 147 current: chain 'B' and resid 267 through 269 Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 186 removed outlier: 3.601A pdb=" N SER B 120 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA B 119 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE B 47 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA B 121 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N THR B 41 " --> pdb=" O HIS B 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 51 through 54 current: chain 'B' and resid 101 through 110 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB5, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AB6, first strand: chain 'B' and resid 296 through 306 removed outlier: 5.492A pdb=" N ASP B 298 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA B 321 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL B 315 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AB8, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AB9, first strand: chain 'C' and resid 2 through 8 removed outlier: 6.111A pdb=" N VAL C 163 " --> pdb=" O HIS C 152 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N HIS C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 14 through 19 removed outlier: 4.384A pdb=" N GLU C 30 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS C 132 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL C 36 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER C 130 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU C 38 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N SER C 128 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR C 126 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU C 42 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA C 124 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU C 44 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR C 122 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR C 46 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N SER C 120 " --> pdb=" O TYR C 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 140 through 147 current: chain 'C' and resid 184 through 185 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 184 through 185 current: chain 'C' and resid 267 through 269 Processing sheet with id=AC2, first strand: chain 'C' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 54 current: chain 'C' and resid 101 through 110 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC4, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AC5, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AC6, first strand: chain 'C' and resid 297 through 306 removed outlier: 6.078A pdb=" N ASP C 298 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA C 321 " --> pdb=" O ASP C 298 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL C 315 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AC8, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AC9, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AD1, first strand: chain 'D' and resid 14 through 19 removed outlier: 3.679A pdb=" N GLU D 30 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS D 132 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL D 36 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER D 130 " --> pdb=" O VAL D 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 140 through 147 current: chain 'D' and resid 267 through 269 Processing sheet with id=AD2, first strand: chain 'D' and resid 183 through 186 removed outlier: 6.661A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA D 121 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR D 41 " --> pdb=" O HIS D 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 51 through 54 current: chain 'D' and resid 101 through 110 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AD5, first strand: chain 'D' and resid 220 through 221 Processing sheet with id=AD6, first strand: chain 'D' and resid 296 through 305 removed outlier: 5.557A pdb=" N ASP D 298 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA D 321 " --> pdb=" O ASP D 298 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL D 315 " --> pdb=" O PRO D 304 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 326 through 329 Processing sheet with id=AD8, first strand: chain 'D' and resid 331 through 332 Processing sheet with id=AD9, first strand: chain 'D' and resid 387 through 388 Processing sheet with id=AE1, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AE2, first strand: chain 'E' and resid 34 through 38 removed outlier: 8.629A pdb=" N LEU E 34 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER E 51 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG E 36 " --> pdb=" O GLN E 49 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N SER E 51 " --> pdb=" O MET E 70 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N MET E 70 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS E 66 " --> pdb=" O GLY E 55 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 84 through 86 removed outlier: 4.079A pdb=" N GLU E 109 " --> pdb=" O PHE E 129 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 149 through 156 Processing sheet with id=AE5, first strand: chain 'E' and resid 236 through 237 removed outlier: 3.666A pdb=" N VAL E 169 " --> pdb=" O GLY E 253 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY E 253 " --> pdb=" O VAL E 169 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 175 through 176 Processing sheet with id=AE7, first strand: chain 'E' and resid 183 through 184 Processing sheet with id=AE8, first strand: chain 'E' and resid 275 through 279 Processing sheet with id=AE9, first strand: chain 'F' and resid 17 through 19 Processing sheet with id=AF1, first strand: chain 'F' and resid 34 through 38 removed outlier: 8.752A pdb=" N LEU F 34 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER F 51 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG F 36 " --> pdb=" O GLN F 49 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N SER F 51 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N MET F 70 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS F 66 " --> pdb=" O GLY F 55 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N LYS F 57 " --> pdb=" O TRP F 64 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N TRP F 64 " --> pdb=" O LYS F 57 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 84 through 86 removed outlier: 5.442A pdb=" N PHE F 129 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N THR F 112 " --> pdb=" O HIS F 127 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N HIS F 127 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLY F 114 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N CYS F 125 " --> pdb=" O GLY F 114 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N THR F 116 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS F 123 " --> pdb=" O THR F 116 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 149 through 156 Processing sheet with id=AF4, first strand: chain 'F' and resid 236 through 237 Processing sheet with id=AF5, first strand: chain 'F' and resid 175 through 176 Processing sheet with id=AF6, first strand: chain 'F' and resid 181 through 184 Processing sheet with id=AF7, first strand: chain 'F' and resid 275 through 279 Processing sheet with id=AF8, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AF9, first strand: chain 'G' and resid 34 through 38 removed outlier: 8.453A pdb=" N LEU G 34 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER G 51 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 10.199A pdb=" N SER G 51 " --> pdb=" O MET G 70 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N MET G 70 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS G 66 " --> pdb=" O GLY G 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 74 through 79 current: chain 'G' and resid 90 through 104 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 90 through 104 current: chain 'G' and resid 122 through 131 Processing sheet with id=AG1, first strand: chain 'G' and resid 148 through 156 Processing sheet with id=AG2, first strand: chain 'G' and resid 236 through 237 removed outlier: 3.571A pdb=" N VAL G 169 " --> pdb=" O GLY G 253 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 175 through 176 Processing sheet with id=AG4, first strand: chain 'G' and resid 183 through 184 Processing sheet with id=AG5, first strand: chain 'G' and resid 275 through 279 removed outlier: 3.879A pdb=" N GLN G 282 " --> pdb=" O GLY G 279 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AG7, first strand: chain 'H' and resid 34 through 38 removed outlier: 8.699A pdb=" N LEU H 34 " --> pdb=" O SER H 51 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER H 51 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG H 36 " --> pdb=" O GLN H 49 " (cutoff:3.500A) removed outlier: 10.430A pdb=" N SER H 51 " --> pdb=" O MET H 70 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N MET H 70 " --> pdb=" O SER H 51 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LYS H 66 " --> pdb=" O GLY H 55 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 84 through 86 removed outlier: 4.241A pdb=" N GLU H 109 " --> pdb=" O PHE H 129 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 149 through 156 Processing sheet with id=AH1, first strand: chain 'H' and resid 236 through 237 Processing sheet with id=AH2, first strand: chain 'H' and resid 175 through 176 Processing sheet with id=AH3, first strand: chain 'H' and resid 183 through 184 Processing sheet with id=AH4, first strand: chain 'H' and resid 275 through 279 Processing sheet with id=AH5, first strand: chain 'I' and resid 143 through 144 removed outlier: 6.432A pdb=" N PHE I 115 " --> pdb=" O TYR I 126 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR I 126 " --> pdb=" O PHE I 115 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL I 117 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR I 126 " --> pdb=" O PRO I 137 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 185 through 188 removed outlier: 9.578A pdb=" N ALA I 193 " --> pdb=" O PRO I 204 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 200 through 204 current: chain 'I' and resid 224 through 234 removed outlier: 8.322A pdb=" N VAL I 225 " --> pdb=" O TRP I 245 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TRP I 245 " --> pdb=" O VAL I 225 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER I 241 " --> pdb=" O LEU I 229 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY I 231 " --> pdb=" O ALA I 239 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA I 239 " --> pdb=" O GLY I 231 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASN I 233 " --> pdb=" O ARG I 237 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG I 237 " --> pdb=" O ASN I 233 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 128 through 130 Processing sheet with id=AH8, first strand: chain 'J' and resid 185 through 189 removed outlier: 8.616A pdb=" N ALA J 193 " --> pdb=" O PRO J 204 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 200 through 204 current: chain 'J' and resid 224 through 234 removed outlier: 7.941A pdb=" N VAL J 225 " --> pdb=" O TRP J 245 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TRP J 245 " --> pdb=" O VAL J 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER J 241 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY J 231 " --> pdb=" O ALA J 239 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA J 239 " --> pdb=" O GLY J 231 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASN J 233 " --> pdb=" O ARG J 237 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG J 237 " --> pdb=" O ASN J 233 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 114 through 119 removed outlier: 5.757A pdb=" N HIS K 119 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL K 123 " --> pdb=" O HIS K 119 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 185 through 189 removed outlier: 4.183A pdb=" N GLY K 185 " --> pdb=" O TYR K 196 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N ALA K 193 " --> pdb=" O PRO K 204 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 201 through 204 current: chain 'K' and resid 224 through 234 removed outlier: 8.286A pdb=" N VAL K 225 " --> pdb=" O TRP K 245 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TRP K 245 " --> pdb=" O VAL K 225 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER K 241 " --> pdb=" O LEU K 229 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY K 231 " --> pdb=" O ALA K 239 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA K 239 " --> pdb=" O GLY K 231 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASN K 233 " --> pdb=" O ARG K 237 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG K 237 " --> pdb=" O ASN K 233 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 143 through 144 removed outlier: 7.580A pdb=" N TYR L 126 " --> pdb=" O PRO L 137 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 185 through 188 removed outlier: 9.338A pdb=" N ALA L 193 " --> pdb=" O PRO L 204 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 200 through 204 current: chain 'L' and resid 224 through 233 removed outlier: 8.366A pdb=" N VAL L 225 " --> pdb=" O TRP L 245 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TRP L 245 " --> pdb=" O VAL L 225 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER L 241 " --> pdb=" O LEU L 229 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY L 231 " --> pdb=" O ALA L 239 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA L 239 " --> pdb=" O GLY L 231 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASN L 233 " --> pdb=" O ARG L 237 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ARG L 237 " --> pdb=" O ASN L 233 " (cutoff:3.500A) 1066 hydrogen bonds defined for protein. 2706 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: 6.46 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8124 1.33 - 1.46: 8502 1.46 - 1.59: 14950 1.59 - 1.72: 0 1.72 - 1.85: 332 Bond restraints: 31908 Sorted by residual: bond pdb=" CA PRO F 172 " pdb=" C PRO F 172 " ideal model delta sigma weight residual 1.517 1.561 -0.044 6.70e-03 2.23e+04 4.23e+01 bond pdb=" CA LEU A 397 " pdb=" C LEU A 397 " ideal model delta sigma weight residual 1.528 1.457 0.071 1.11e-02 8.12e+03 4.12e+01 bond pdb=" CA PRO G 172 " pdb=" C PRO G 172 " ideal model delta sigma weight residual 1.517 1.566 -0.049 9.30e-03 1.16e+04 2.77e+01 bond pdb=" CA ASP A 183 " pdb=" C ASP A 183 " ideal model delta sigma weight residual 1.520 1.472 0.049 1.20e-02 6.94e+03 1.65e+01 bond pdb=" CA TYR A 180 " pdb=" C TYR A 180 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.37e-02 5.33e+03 1.62e+01 ... (remaining 31903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 42294 3.14 - 6.29: 894 6.29 - 9.43: 262 9.43 - 12.57: 7 12.57 - 15.72: 3 Bond angle restraints: 43460 Sorted by residual: angle pdb=" N TYR A 180 " pdb=" CA TYR A 180 " pdb=" C TYR A 180 " ideal model delta sigma weight residual 109.95 94.23 15.72 1.44e+00 4.82e-01 1.19e+02 angle pdb=" N ASP H 250 " pdb=" CA ASP H 250 " pdb=" C ASP H 250 " ideal model delta sigma weight residual 111.36 122.79 -11.43 1.09e+00 8.42e-01 1.10e+02 angle pdb=" N ASN H 5 " pdb=" CA ASN H 5 " pdb=" C ASN H 5 " ideal model delta sigma weight residual 112.92 100.25 12.67 1.23e+00 6.61e-01 1.06e+02 angle pdb=" N VAL H 8 " pdb=" CA VAL H 8 " pdb=" C VAL H 8 " ideal model delta sigma weight residual 113.10 103.75 9.35 9.70e-01 1.06e+00 9.29e+01 angle pdb=" C TYR C 189 " pdb=" N PRO C 190 " pdb=" CA PRO C 190 " ideal model delta sigma weight residual 119.66 126.50 -6.84 7.20e-01 1.93e+00 9.04e+01 ... (remaining 43455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 18581 17.94 - 35.87: 480 35.87 - 53.81: 129 53.81 - 71.74: 57 71.74 - 89.68: 24 Dihedral angle restraints: 19271 sinusoidal: 7551 harmonic: 11720 Sorted by residual: dihedral pdb=" CB CYS C 62 " pdb=" SG CYS C 62 " pdb=" SG CYS C 94 " pdb=" CB CYS C 94 " ideal model delta sinusoidal sigma weight residual 93.00 -178.03 -88.97 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS A 328 " pdb=" SG CYS A 328 " pdb=" SG CYS A 370 " pdb=" CB CYS A 370 " ideal model delta sinusoidal sigma weight residual 93.00 171.52 -78.52 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual 93.00 167.09 -74.09 1 1.00e+01 1.00e-02 6.97e+01 ... (remaining 19268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4654 0.116 - 0.232: 215 0.232 - 0.349: 12 0.349 - 0.465: 1 0.465 - 0.581: 2 Chirality restraints: 4884 Sorted by residual: chirality pdb=" CA GLU F 168 " pdb=" N GLU F 168 " pdb=" C GLU F 168 " pdb=" CB GLU F 168 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.44e+00 chirality pdb=" CA ILE A 402 " pdb=" N ILE A 402 " pdb=" C ILE A 402 " pdb=" CB ILE A 402 " both_signs ideal model delta sigma weight residual False 2.43 1.91 0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" CA ARG G 251 " pdb=" N ARG G 251 " pdb=" C ARG G 251 " pdb=" CB ARG G 251 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 4881 not shown) Planarity restraints: 5616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP L 261 " -0.029 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C TRP L 261 " 0.101 2.00e-02 2.50e+03 pdb=" O TRP L 261 " -0.036 2.00e-02 2.50e+03 pdb=" OXT TRP L 261 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP K 261 " 0.028 2.00e-02 2.50e+03 5.64e-02 3.18e+01 pdb=" C TRP K 261 " -0.098 2.00e-02 2.50e+03 pdb=" O TRP K 261 " 0.035 2.00e-02 2.50e+03 pdb=" OXT TRP K 261 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP I 261 " -0.027 2.00e-02 2.50e+03 5.53e-02 3.06e+01 pdb=" C TRP I 261 " 0.096 2.00e-02 2.50e+03 pdb=" O TRP I 261 " -0.035 2.00e-02 2.50e+03 pdb=" OXT TRP I 261 " -0.034 2.00e-02 2.50e+03 ... (remaining 5613 not shown) Histogram of nonbonded interaction distances: 0.69 - 1.53: 3 1.53 - 2.37: 12 2.37 - 3.21: 28302 3.21 - 4.06: 78924 4.06 - 4.90: 142270 Warning: very small nonbonded interaction distances. Nonbonded interactions: 249511 Sorted by model distance: nonbonded pdb=" OE2 GLU E 168 " pdb=" NH2 ARG E 251 " model vdw 0.687 3.120 nonbonded pdb=" CD GLU E 168 " pdb=" NH2 ARG E 251 " model vdw 1.136 3.350 nonbonded pdb=" CG GLU E 168 " pdb=" NH1 ARG E 251 " model vdw 1.175 3.520 nonbonded pdb=" CD GLU E 168 " pdb=" CZ ARG E 251 " model vdw 1.578 3.500 nonbonded pdb=" OE2 GLU E 168 " pdb=" CZ ARG E 251 " model vdw 1.613 3.270 ... (remaining 249506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.450 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: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.260 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 : 0.010 0.227 31965 Z= 0.593 Angle : 1.287 15.719 43574 Z= 0.906 Chirality : 0.058 0.581 4884 Planarity : 0.005 0.091 5616 Dihedral : 9.953 89.679 11580 Min Nonbonded Distance : 0.687 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.62 % Favored : 98.11 % Rotamer: Outliers : 0.38 % Allowed : 0.88 % Favored : 98.75 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.13), residues: 4020 helix: 0.40 (0.22), residues: 449 sheet: 1.25 (0.14), residues: 1259 loop : 1.25 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 68 TYR 0.020 0.003 TYR H 288 PHE 0.014 0.002 PHE H 6 TRP 0.021 0.003 TRP K 189 HIS 0.007 0.001 HIS F 170 Details of bonding type rmsd covalent geometry : bond 0.01017 (31908) covalent geometry : angle 1.26439 (43460) SS BOND : bond 0.05872 ( 57) SS BOND : angle 4.83366 ( 114) hydrogen bonds : bond 0.16977 ( 1066) hydrogen bonds : angle 7.96776 ( 2706) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 714 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 THR cc_start: 0.8220 (m) cc_final: 0.7997 (m) REVERT: A 400 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: B 24 TYR cc_start: 0.7929 (m-80) cc_final: 0.7650 (m-80) REVERT: B 30 GLU cc_start: 0.8139 (tt0) cc_final: 0.7890 (tt0) REVERT: B 128 SER cc_start: 0.8880 (m) cc_final: 0.8483 (p) REVERT: B 152 HIS cc_start: 0.8499 (t70) cc_final: 0.7680 (t-90) REVERT: B 264 ASN cc_start: 0.9339 (t0) cc_final: 0.8988 (t0) REVERT: B 281 ASP cc_start: 0.7882 (t0) cc_final: 0.7437 (t70) REVERT: B 366 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7693 (mtp85) REVERT: C 79 LYS cc_start: 0.8496 (tttp) cc_final: 0.8250 (ttmt) REVERT: C 138 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7499 (mm-40) REVERT: C 158 ASP cc_start: 0.8778 (m-30) cc_final: 0.8520 (m-30) REVERT: C 212 ASP cc_start: 0.8103 (t0) cc_final: 0.7888 (p0) REVERT: C 311 ASP cc_start: 0.7631 (t0) cc_final: 0.7384 (t0) REVERT: D 21 ARG cc_start: 0.7423 (ttt180) cc_final: 0.5335 (ttt180) REVERT: D 128 SER cc_start: 0.9006 (m) cc_final: 0.8634 (p) REVERT: D 132 LYS cc_start: 0.8497 (tttt) cc_final: 0.8228 (ttmm) REVERT: D 157 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8575 (mmmm) REVERT: D 212 ASP cc_start: 0.8071 (t0) cc_final: 0.7262 (p0) REVERT: E 64 TRP cc_start: 0.8390 (p-90) cc_final: 0.8059 (p-90) REVERT: E 97 MET cc_start: 0.9086 (tmt) cc_final: 0.7995 (tmt) REVERT: E 192 VAL cc_start: 0.7899 (p) cc_final: 0.7450 (t) REVERT: E 193 ASN cc_start: 0.7952 (m-40) cc_final: 0.7396 (m-40) REVERT: E 195 GLN cc_start: 0.8071 (mt0) cc_final: 0.7266 (pm20) REVERT: E 403 THR cc_start: 0.6706 (m) cc_final: 0.6410 (p) REVERT: F 171 MET cc_start: 0.9058 (tpt) cc_final: 0.8806 (tpp) REVERT: F 372 SER cc_start: 0.8730 (t) cc_final: 0.8459 (p) REVERT: G 188 VAL cc_start: 0.8467 (t) cc_final: 0.8039 (m) REVERT: G 200 LYS cc_start: 0.8427 (pttt) cc_final: 0.7941 (tttp) REVERT: G 313 HIS cc_start: 0.8169 (p90) cc_final: 0.7781 (m90) REVERT: H 179 THR cc_start: 0.8854 (m) cc_final: 0.8646 (p) REVERT: H 193 ASN cc_start: 0.8727 (m-40) cc_final: 0.8323 (t0) REVERT: I 122 LYS cc_start: 0.7977 (pttt) cc_final: 0.7299 (tmtt) REVERT: J 136 LYS cc_start: 0.8769 (pttp) cc_final: 0.8478 (ptmm) REVERT: J 186 TYR cc_start: 0.7999 (m-80) cc_final: 0.7782 (m-80) REVERT: K 196 TYR cc_start: 0.6118 (t80) cc_final: 0.5570 (t80) REVERT: L 115 PHE cc_start: 0.8523 (m-80) cc_final: 0.8292 (m-80) REVERT: L 172 LYS cc_start: 0.8316 (mmtm) cc_final: 0.7822 (mmtm) outliers start: 13 outliers final: 6 residues processed: 724 average time/residue: 0.2151 time to fit residues: 237.5530 Evaluate side-chains 395 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 388 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain F residue 6 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0010 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS B 175 ASN B 252 GLN C 351 GLN D 252 GLN ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN F 127 HIS ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 HIS H 62 HIS H 170 HIS J 191 HIS K 119 HIS ** K 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 HIS L 246 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.123914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.084231 restraints weight = 55202.508| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.70 r_work: 0.2987 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31965 Z= 0.180 Angle : 0.620 15.365 43574 Z= 0.334 Chirality : 0.046 0.206 4884 Planarity : 0.005 0.065 5616 Dihedral : 5.624 84.522 4379 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.34 % Favored : 98.48 % Rotamer: Outliers : 1.46 % Allowed : 6.86 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.13), residues: 4020 helix: 1.86 (0.24), residues: 454 sheet: 1.20 (0.14), residues: 1302 loop : 0.69 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 251 TYR 0.015 0.002 TYR L 196 PHE 0.029 0.002 PHE E 410 TRP 0.019 0.001 TRP L 189 HIS 0.013 0.001 HIS F 226 Details of bonding type rmsd covalent geometry : bond 0.00427 (31908) covalent geometry : angle 0.61640 (43460) SS BOND : bond 0.00519 ( 57) SS BOND : angle 1.39220 ( 114) hydrogen bonds : bond 0.04377 ( 1066) hydrogen bonds : angle 6.02984 ( 2706) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 424 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8420 (ttm) cc_final: 0.8122 (ttm) REVERT: B 9 ASN cc_start: 0.8995 (t0) cc_final: 0.8548 (t0) REVERT: B 30 GLU cc_start: 0.8567 (tt0) cc_final: 0.8015 (tt0) REVERT: B 128 SER cc_start: 0.8891 (m) cc_final: 0.8401 (p) REVERT: B 152 HIS cc_start: 0.8403 (t70) cc_final: 0.7452 (t-90) REVERT: B 264 ASN cc_start: 0.9453 (t0) cc_final: 0.9155 (t0) REVERT: B 366 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7675 (mtp85) REVERT: B 407 MET cc_start: 0.7138 (ppp) cc_final: 0.6840 (ppp) REVERT: C 2 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8469 (tp30) REVERT: C 79 LYS cc_start: 0.8647 (tttp) cc_final: 0.8348 (ttmt) REVERT: C 187 MET cc_start: 0.8951 (ttt) cc_final: 0.8734 (ttm) REVERT: C 212 ASP cc_start: 0.8554 (t0) cc_final: 0.8042 (p0) REVERT: C 311 ASP cc_start: 0.8118 (t0) cc_final: 0.7851 (t0) REVERT: C 341 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: D 72 ASN cc_start: 0.8377 (p0) cc_final: 0.8110 (p0) REVERT: D 88 MET cc_start: 0.8568 (mmm) cc_final: 0.8318 (mtp) REVERT: D 132 LYS cc_start: 0.8618 (tttt) cc_final: 0.8277 (ttmm) REVERT: D 212 ASP cc_start: 0.8426 (t0) cc_final: 0.7565 (p0) REVERT: D 401 ASP cc_start: 0.7192 (m-30) cc_final: 0.6854 (m-30) REVERT: E 64 TRP cc_start: 0.8520 (p-90) cc_final: 0.8124 (p-90) REVERT: E 171 MET cc_start: 0.9078 (ttm) cc_final: 0.8550 (tpp) REVERT: E 195 GLN cc_start: 0.8136 (mt0) cc_final: 0.7572 (mp10) REVERT: E 247 GLU cc_start: 0.8574 (pm20) cc_final: 0.8232 (pt0) REVERT: E 403 THR cc_start: 0.7225 (m) cc_final: 0.6894 (p) REVERT: G 200 LYS cc_start: 0.8056 (pttt) cc_final: 0.7847 (tttp) REVERT: G 313 HIS cc_start: 0.8429 (p90) cc_final: 0.7626 (m90) REVERT: G 354 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8418 (mt-10) REVERT: H 70 MET cc_start: 0.8911 (tpt) cc_final: 0.8537 (tpt) REVERT: H 193 ASN cc_start: 0.8771 (m-40) cc_final: 0.8348 (t0) REVERT: H 224 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7519 (tm-30) REVERT: H 247 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8543 (tt0) REVERT: H 401 GLU cc_start: 0.8307 (tp30) cc_final: 0.7818 (tp30) REVERT: I 122 LYS cc_start: 0.7921 (pttt) cc_final: 0.7673 (mttt) REVERT: I 134 VAL cc_start: 0.7554 (t) cc_final: 0.7209 (m) REVERT: I 135 MET cc_start: 0.7289 (mtt) cc_final: 0.5969 (tpt) REVERT: J 126 TYR cc_start: 0.8505 (m-80) cc_final: 0.7740 (m-80) REVERT: J 247 LYS cc_start: 0.8041 (tptp) cc_final: 0.7700 (tptp) REVERT: K 135 MET cc_start: 0.5942 (mmp) cc_final: 0.5740 (mmp) REVERT: K 189 TRP cc_start: 0.7787 (p-90) cc_final: 0.7574 (p-90) outliers start: 50 outliers final: 33 residues processed: 450 average time/residue: 0.2080 time to fit residues: 149.2623 Evaluate side-chains 401 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 366 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain F residue 127 HIS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain G residue 369 VAL Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 301 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 277 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 317 optimal weight: 7.9990 chunk 358 optimal weight: 10.0000 chunk 356 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS E 127 HIS F 62 HIS ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 GLN H 18 HIS ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 HIS K 146 ASN ** L 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.121855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.082002 restraints weight = 55404.095| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.62 r_work: 0.2923 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 31965 Z= 0.204 Angle : 0.577 11.622 43574 Z= 0.309 Chirality : 0.046 0.162 4884 Planarity : 0.004 0.045 5616 Dihedral : 5.510 88.726 4372 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.19 % Favored : 97.66 % Rotamer: Outliers : 2.30 % Allowed : 7.88 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.13), residues: 4020 helix: 2.20 (0.24), residues: 454 sheet: 0.95 (0.14), residues: 1276 loop : 0.27 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 200 TYR 0.016 0.002 TYR A 122 PHE 0.020 0.002 PHE J 201 TRP 0.028 0.001 TRP L 189 HIS 0.037 0.001 HIS F 127 Details of bonding type rmsd covalent geometry : bond 0.00481 (31908) covalent geometry : angle 0.57409 (43460) SS BOND : bond 0.00403 ( 57) SS BOND : angle 1.22895 ( 114) hydrogen bonds : bond 0.03891 ( 1066) hydrogen bonds : angle 5.43942 ( 2706) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 388 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8547 (mmm) cc_final: 0.8309 (mtp) REVERT: A 97 ASP cc_start: 0.7467 (p0) cc_final: 0.7231 (t70) REVERT: A 212 ASP cc_start: 0.8505 (t0) cc_final: 0.7409 (p0) REVERT: A 276 MET cc_start: 0.8499 (ttm) cc_final: 0.8184 (ttm) REVERT: A 400 GLN cc_start: 0.7701 (pm20) cc_final: 0.6624 (tm-30) REVERT: B 128 SER cc_start: 0.8946 (m) cc_final: 0.8427 (p) REVERT: B 138 GLN cc_start: 0.7715 (pt0) cc_final: 0.7368 (pp30) REVERT: B 140 ASN cc_start: 0.8779 (m-40) cc_final: 0.8261 (m-40) REVERT: B 152 HIS cc_start: 0.8352 (t70) cc_final: 0.7699 (t-90) REVERT: B 166 MET cc_start: 0.9037 (mmm) cc_final: 0.8758 (mmm) REVERT: B 264 ASN cc_start: 0.9469 (t0) cc_final: 0.9175 (t0) REVERT: C 2 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8481 (tp30) REVERT: C 79 LYS cc_start: 0.8710 (tttp) cc_final: 0.8395 (ttmt) REVERT: C 138 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7801 (mm-40) REVERT: C 187 MET cc_start: 0.8924 (ttt) cc_final: 0.8685 (ttm) REVERT: C 212 ASP cc_start: 0.8517 (t0) cc_final: 0.8051 (p0) REVERT: C 242 TYR cc_start: 0.6981 (t80) cc_final: 0.5968 (t80) REVERT: C 311 ASP cc_start: 0.8219 (t0) cc_final: 0.7959 (t0) REVERT: C 319 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8465 (mtmm) REVERT: D 72 ASN cc_start: 0.8382 (p0) cc_final: 0.7967 (p0) REVERT: D 132 LYS cc_start: 0.8531 (tttt) cc_final: 0.8213 (ttmm) REVERT: D 212 ASP cc_start: 0.8304 (t0) cc_final: 0.7401 (p0) REVERT: D 400 GLN cc_start: 0.7452 (pm20) cc_final: 0.7147 (pm20) REVERT: D 401 ASP cc_start: 0.7353 (m-30) cc_final: 0.7113 (m-30) REVERT: D 407 MET cc_start: 0.7496 (ppp) cc_final: 0.7075 (ppp) REVERT: E 195 GLN cc_start: 0.8149 (mt0) cc_final: 0.7586 (mp10) REVERT: E 247 GLU cc_start: 0.8614 (pm20) cc_final: 0.8329 (pt0) REVERT: E 315 LYS cc_start: 0.8704 (tttt) cc_final: 0.8492 (ttmm) REVERT: E 403 THR cc_start: 0.7349 (m) cc_final: 0.7104 (p) REVERT: F 171 MET cc_start: 0.9300 (tpp) cc_final: 0.8878 (tpp) REVERT: F 314 LYS cc_start: 0.7374 (mttt) cc_final: 0.5689 (mttt) REVERT: G 183 GLN cc_start: 0.6024 (OUTLIER) cc_final: 0.5774 (tp-100) REVERT: G 354 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8514 (mt-10) REVERT: G 361 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8439 (mt-10) REVERT: H 193 ASN cc_start: 0.8729 (m-40) cc_final: 0.8342 (t0) REVERT: H 247 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8555 (tt0) REVERT: I 122 LYS cc_start: 0.7944 (pttt) cc_final: 0.7275 (tmtt) REVERT: J 161 ASP cc_start: 0.7885 (t70) cc_final: 0.7667 (t0) REVERT: J 172 LYS cc_start: 0.9012 (mtpt) cc_final: 0.8653 (mttm) REVERT: J 215 ARG cc_start: 0.8368 (mtt-85) cc_final: 0.7416 (mmm-85) REVERT: K 141 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8806 (ptmt) REVERT: K 189 TRP cc_start: 0.7829 (p-90) cc_final: 0.7606 (p-90) REVERT: L 161 ASP cc_start: 0.8559 (t0) cc_final: 0.8256 (t0) REVERT: L 234 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8426 (mt-10) outliers start: 79 outliers final: 48 residues processed: 434 average time/residue: 0.1866 time to fit residues: 130.8691 Evaluate side-chains 401 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 350 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 27 MET Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 396 CYS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain G residue 183 GLN Chi-restraints excluded: chain G residue 390 MET Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 171 MET Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 105 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 284 optimal weight: 3.9990 chunk 337 optimal weight: 8.9990 chunk 225 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 341 optimal weight: 30.0000 chunk 358 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 331 HIS ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS F 127 HIS F 226 HIS ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.121927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082107 restraints weight = 55101.088| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.61 r_work: 0.2924 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31965 Z= 0.161 Angle : 0.551 10.866 43574 Z= 0.290 Chirality : 0.045 0.171 4884 Planarity : 0.004 0.046 5616 Dihedral : 5.425 88.095 4372 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.04 % Favored : 97.84 % Rotamer: Outliers : 1.95 % Allowed : 9.33 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.89 (0.13), residues: 4020 helix: 2.39 (0.25), residues: 448 sheet: 0.86 (0.15), residues: 1247 loop : 0.16 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 366 TYR 0.020 0.001 TYR I 196 PHE 0.017 0.001 PHE J 201 TRP 0.023 0.001 TRP L 189 HIS 0.008 0.001 HIS K 139 Details of bonding type rmsd covalent geometry : bond 0.00381 (31908) covalent geometry : angle 0.54745 (43460) SS BOND : bond 0.00358 ( 57) SS BOND : angle 1.34921 ( 114) hydrogen bonds : bond 0.03452 ( 1066) hydrogen bonds : angle 5.23907 ( 2706) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 360 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.8529 (t0) cc_final: 0.7503 (p0) REVERT: A 276 MET cc_start: 0.8524 (ttm) cc_final: 0.8224 (ttm) REVERT: A 400 GLN cc_start: 0.7639 (pm20) cc_final: 0.6598 (tm-30) REVERT: B 128 SER cc_start: 0.9039 (m) cc_final: 0.8550 (p) REVERT: B 138 GLN cc_start: 0.7631 (pt0) cc_final: 0.7307 (pp30) REVERT: B 140 ASN cc_start: 0.8851 (m-40) cc_final: 0.8308 (m-40) REVERT: B 152 HIS cc_start: 0.8395 (t70) cc_final: 0.7717 (t-90) REVERT: B 166 MET cc_start: 0.9028 (mmm) cc_final: 0.8772 (mmm) REVERT: B 264 ASN cc_start: 0.9469 (t0) cc_final: 0.9166 (t0) REVERT: C 2 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8439 (tp30) REVERT: C 79 LYS cc_start: 0.8703 (tttp) cc_final: 0.8379 (ttmt) REVERT: C 138 GLN cc_start: 0.8095 (mm110) cc_final: 0.7876 (mm-40) REVERT: C 187 MET cc_start: 0.8968 (ttt) cc_final: 0.8758 (ttm) REVERT: C 212 ASP cc_start: 0.8497 (t0) cc_final: 0.8093 (p0) REVERT: C 311 ASP cc_start: 0.8220 (t0) cc_final: 0.7950 (t0) REVERT: C 319 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8460 (mtmm) REVERT: D 72 ASN cc_start: 0.8384 (p0) cc_final: 0.7963 (p0) REVERT: D 132 LYS cc_start: 0.8519 (tttt) cc_final: 0.8213 (ttmm) REVERT: D 212 ASP cc_start: 0.8289 (t0) cc_final: 0.7380 (p0) REVERT: D 400 GLN cc_start: 0.7613 (pm20) cc_final: 0.7282 (pm20) REVERT: D 401 ASP cc_start: 0.7254 (m-30) cc_final: 0.6956 (m-30) REVERT: D 407 MET cc_start: 0.7503 (ppp) cc_final: 0.6938 (ppp) REVERT: E 195 GLN cc_start: 0.8080 (mt0) cc_final: 0.7560 (mp10) REVERT: E 247 GLU cc_start: 0.8524 (pm20) cc_final: 0.8266 (pt0) REVERT: E 315 LYS cc_start: 0.8700 (tttt) cc_final: 0.8480 (ttmm) REVERT: E 403 THR cc_start: 0.7282 (m) cc_final: 0.7031 (p) REVERT: F 171 MET cc_start: 0.9282 (tpp) cc_final: 0.8797 (tpp) REVERT: G 354 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8397 (mt-10) REVERT: G 361 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8427 (mt-10) REVERT: G 388 MET cc_start: 0.5846 (mmp) cc_final: 0.5421 (mtt) REVERT: H 193 ASN cc_start: 0.8762 (m-40) cc_final: 0.8358 (t0) REVERT: H 247 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8530 (tt0) REVERT: I 122 LYS cc_start: 0.7902 (pttt) cc_final: 0.7243 (tmtt) REVERT: J 161 ASP cc_start: 0.7902 (t70) cc_final: 0.7636 (t0) REVERT: J 172 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8564 (mttm) REVERT: J 215 ARG cc_start: 0.8423 (mtt-85) cc_final: 0.7419 (mmm-85) REVERT: K 135 MET cc_start: 0.5750 (mmp) cc_final: 0.5446 (mmt) REVERT: K 141 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8747 (ptmt) REVERT: K 189 TRP cc_start: 0.7837 (p-90) cc_final: 0.7631 (p-90) REVERT: L 161 ASP cc_start: 0.8588 (t0) cc_final: 0.8282 (t0) REVERT: L 234 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8387 (mt-10) outliers start: 67 outliers final: 49 residues processed: 401 average time/residue: 0.1871 time to fit residues: 123.5155 Evaluate side-chains 403 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 352 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 27 MET Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 396 CYS Chi-restraints excluded: chain F residue 127 HIS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 242 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 122 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 386 optimal weight: 4.9990 chunk 346 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 312 optimal weight: 8.9990 chunk 318 optimal weight: 30.0000 chunk 206 optimal weight: 10.0000 chunk 359 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 chunk 193 optimal weight: 30.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 308 HIS A 394 HIS C 252 GLN D 375 HIS ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 HIS K 139 HIS K 220 ASN ** L 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.115399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.075677 restraints weight = 55581.642| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.59 r_work: 0.2839 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 31965 Z= 0.367 Angle : 0.685 8.999 43574 Z= 0.362 Chirality : 0.050 0.201 4884 Planarity : 0.005 0.058 5616 Dihedral : 5.928 86.681 4371 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.31 % Favored : 96.59 % Rotamer: Outliers : 2.89 % Allowed : 9.80 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.32 (0.13), residues: 4020 helix: 1.89 (0.24), residues: 457 sheet: 0.53 (0.15), residues: 1248 loop : -0.27 (0.12), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 13 TYR 0.027 0.002 TYR C 242 PHE 0.019 0.002 PHE B 365 TRP 0.027 0.002 TRP L 189 HIS 0.034 0.002 HIS F 127 Details of bonding type rmsd covalent geometry : bond 0.00885 (31908) covalent geometry : angle 0.68218 (43460) SS BOND : bond 0.00738 ( 57) SS BOND : angle 1.45620 ( 114) hydrogen bonds : bond 0.03967 ( 1066) hydrogen bonds : angle 5.47466 ( 2706) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 359 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: A 207 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8687 (p) REVERT: A 212 ASP cc_start: 0.8429 (t0) cc_final: 0.7510 (p0) REVERT: A 345 GLU cc_start: 0.8439 (mp0) cc_final: 0.8184 (mp0) REVERT: A 400 GLN cc_start: 0.7704 (pm20) cc_final: 0.6689 (tm-30) REVERT: B 128 SER cc_start: 0.8948 (m) cc_final: 0.8464 (p) REVERT: B 138 GLN cc_start: 0.7738 (pt0) cc_final: 0.7514 (pp30) REVERT: B 140 ASN cc_start: 0.8869 (m-40) cc_final: 0.8437 (m-40) REVERT: B 166 MET cc_start: 0.9047 (mmm) cc_final: 0.8822 (mmm) REVERT: B 264 ASN cc_start: 0.9466 (t0) cc_final: 0.9196 (t0) REVERT: C 2 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8423 (tp30) REVERT: C 72 ASN cc_start: 0.9089 (t0) cc_final: 0.8737 (t0) REVERT: C 79 LYS cc_start: 0.8706 (tttp) cc_final: 0.8301 (ttmt) REVERT: C 187 MET cc_start: 0.8927 (ttt) cc_final: 0.8664 (ttm) REVERT: C 212 ASP cc_start: 0.8473 (t0) cc_final: 0.8070 (p0) REVERT: C 311 ASP cc_start: 0.8362 (t0) cc_final: 0.8069 (t0) REVERT: D 72 ASN cc_start: 0.8417 (p0) cc_final: 0.8208 (p0) REVERT: D 132 LYS cc_start: 0.8486 (tttt) cc_final: 0.8196 (ttmm) REVERT: D 212 ASP cc_start: 0.8355 (t0) cc_final: 0.7424 (p0) REVERT: D 400 GLN cc_start: 0.7815 (pm20) cc_final: 0.7450 (pm20) REVERT: D 401 ASP cc_start: 0.7706 (m-30) cc_final: 0.7384 (m-30) REVERT: D 407 MET cc_start: 0.7656 (ppp) cc_final: 0.7094 (ppp) REVERT: E 195 GLN cc_start: 0.8244 (mt0) cc_final: 0.7409 (pm20) REVERT: E 247 GLU cc_start: 0.8767 (pm20) cc_final: 0.8523 (pt0) REVERT: E 403 THR cc_start: 0.7342 (m) cc_final: 0.6915 (p) REVERT: F 254 LYS cc_start: 0.8722 (mttt) cc_final: 0.8138 (mtpp) REVERT: G 354 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8348 (mt-10) REVERT: G 361 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8423 (mt-10) REVERT: H 181 MET cc_start: 0.7817 (mmt) cc_final: 0.7311 (mmm) REVERT: H 193 ASN cc_start: 0.8835 (m-40) cc_final: 0.8357 (t0) REVERT: H 247 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8620 (tt0) REVERT: I 122 LYS cc_start: 0.7903 (pttt) cc_final: 0.7237 (tmtt) REVERT: I 135 MET cc_start: 0.7038 (mtt) cc_final: 0.6016 (mpp) REVERT: J 172 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8545 (mttm) REVERT: K 141 LYS cc_start: 0.8964 (ttpt) cc_final: 0.8701 (ptmt) REVERT: K 151 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8204 (pttt) REVERT: K 209 LYS cc_start: 0.8629 (mmtm) cc_final: 0.8217 (ptpt) REVERT: L 115 PHE cc_start: 0.8460 (m-80) cc_final: 0.8186 (m-80) REVERT: L 161 ASP cc_start: 0.8547 (t0) cc_final: 0.8289 (t0) REVERT: L 234 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8388 (mt-10) outliers start: 99 outliers final: 77 residues processed: 430 average time/residue: 0.1885 time to fit residues: 132.2241 Evaluate side-chains 424 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 345 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 27 MET Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain F residue 127 HIS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 369 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 139 HIS Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 247 LYS Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 212 ASP Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 242 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 315 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 282 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 360 optimal weight: 3.9990 chunk 359 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 305 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS H 195 GLN J 146 ASN K 119 HIS K 139 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.120858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.081342 restraints weight = 55042.840| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.60 r_work: 0.2899 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31965 Z= 0.133 Angle : 0.545 9.381 43574 Z= 0.285 Chirality : 0.045 0.172 4884 Planarity : 0.004 0.049 5616 Dihedral : 5.512 85.403 4371 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.34 % Favored : 97.56 % Rotamer: Outliers : 2.10 % Allowed : 11.38 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.48 (0.13), residues: 4020 helix: 2.22 (0.25), residues: 456 sheet: 0.56 (0.15), residues: 1247 loop : -0.16 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 366 TYR 0.031 0.001 TYR C 242 PHE 0.024 0.001 PHE J 201 TRP 0.026 0.001 TRP L 189 HIS 0.033 0.001 HIS K 139 Details of bonding type rmsd covalent geometry : bond 0.00312 (31908) covalent geometry : angle 0.54195 (43460) SS BOND : bond 0.00287 ( 57) SS BOND : angle 1.18154 ( 114) hydrogen bonds : bond 0.03285 ( 1066) hydrogen bonds : angle 5.16709 ( 2706) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 358 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8478 (p) REVERT: A 211 LYS cc_start: 0.8948 (mmmt) cc_final: 0.8628 (mmtt) REVERT: A 212 ASP cc_start: 0.8401 (t0) cc_final: 0.7529 (p0) REVERT: A 276 MET cc_start: 0.8364 (ttm) cc_final: 0.8099 (ttm) REVERT: A 345 GLU cc_start: 0.8499 (mp0) cc_final: 0.8201 (mp0) REVERT: A 400 GLN cc_start: 0.7592 (pm20) cc_final: 0.6668 (tm-30) REVERT: B 128 SER cc_start: 0.8921 (m) cc_final: 0.8485 (p) REVERT: B 138 GLN cc_start: 0.7652 (pt0) cc_final: 0.7438 (pp30) REVERT: B 140 ASN cc_start: 0.8926 (m-40) cc_final: 0.8499 (m-40) REVERT: B 166 MET cc_start: 0.9040 (mmm) cc_final: 0.8827 (mmm) REVERT: B 264 ASN cc_start: 0.9493 (t0) cc_final: 0.9197 (t0) REVERT: C 2 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8415 (tp30) REVERT: C 79 LYS cc_start: 0.8766 (tttp) cc_final: 0.8390 (ttmt) REVERT: C 187 MET cc_start: 0.8914 (ttt) cc_final: 0.8694 (ttm) REVERT: C 212 ASP cc_start: 0.8415 (t0) cc_final: 0.8060 (p0) REVERT: C 311 ASP cc_start: 0.8227 (t0) cc_final: 0.7936 (t0) REVERT: D 72 ASN cc_start: 0.8378 (p0) cc_final: 0.7936 (p0) REVERT: D 132 LYS cc_start: 0.8418 (tttt) cc_final: 0.8120 (ttmm) REVERT: D 212 ASP cc_start: 0.8310 (t0) cc_final: 0.7405 (p0) REVERT: D 302 GLU cc_start: 0.8243 (tp30) cc_final: 0.8033 (tt0) REVERT: D 400 GLN cc_start: 0.7714 (pm20) cc_final: 0.7331 (pm20) REVERT: D 401 ASP cc_start: 0.7436 (m-30) cc_final: 0.7110 (m-30) REVERT: D 407 MET cc_start: 0.7589 (ppp) cc_final: 0.7038 (ppp) REVERT: E 192 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7812 (t) REVERT: E 195 GLN cc_start: 0.8183 (mt0) cc_final: 0.7397 (pm20) REVERT: E 247 GLU cc_start: 0.8705 (pm20) cc_final: 0.8434 (pt0) REVERT: E 403 THR cc_start: 0.7166 (m) cc_final: 0.6666 (p) REVERT: F 171 MET cc_start: 0.9280 (tpp) cc_final: 0.8848 (tpp) REVERT: F 254 LYS cc_start: 0.8678 (mttt) cc_final: 0.8078 (mtpp) REVERT: G 200 LYS cc_start: 0.8104 (ptmt) cc_final: 0.7875 (tttp) REVERT: G 354 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8323 (mt-10) REVERT: G 361 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8452 (mt-10) REVERT: G 388 MET cc_start: 0.5825 (mmp) cc_final: 0.5398 (mtm) REVERT: H 193 ASN cc_start: 0.8846 (m-40) cc_final: 0.8382 (t0) REVERT: H 247 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8565 (tt0) REVERT: I 122 LYS cc_start: 0.7852 (pttt) cc_final: 0.7157 (tmtt) REVERT: I 135 MET cc_start: 0.7027 (mtt) cc_final: 0.5973 (mpp) REVERT: I 195 GLN cc_start: 0.7050 (tm-30) cc_final: 0.6778 (tm-30) REVERT: K 135 MET cc_start: 0.5475 (mpp) cc_final: 0.4807 (mpp) REVERT: K 141 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8613 (ptmt) REVERT: K 151 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8131 (pttt) REVERT: K 209 LYS cc_start: 0.8667 (mmtm) cc_final: 0.8290 (ptpt) REVERT: L 115 PHE cc_start: 0.8504 (m-80) cc_final: 0.8224 (m-80) REVERT: L 161 ASP cc_start: 0.8573 (t0) cc_final: 0.8302 (t0) REVERT: L 212 ASP cc_start: 0.6713 (OUTLIER) cc_final: 0.6030 (p0) outliers start: 72 outliers final: 50 residues processed: 407 average time/residue: 0.1956 time to fit residues: 129.8501 Evaluate side-chains 397 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 342 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 27 MET Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 127 HIS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 247 GLU Chi-restraints excluded: chain G residue 291 HIS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 397 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 139 HIS Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 212 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 106 optimal weight: 9.9990 chunk 361 optimal weight: 20.0000 chunk 284 optimal weight: 4.9990 chunk 188 optimal weight: 20.0000 chunk 320 optimal weight: 10.0000 chunk 311 optimal weight: 8.9990 chunk 296 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS J 146 ASN K 139 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.116253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.076607 restraints weight = 55412.115| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.59 r_work: 0.2858 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 31965 Z= 0.276 Angle : 0.605 10.108 43574 Z= 0.316 Chirality : 0.047 0.185 4884 Planarity : 0.005 0.051 5616 Dihedral : 5.580 86.546 4368 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 2.57 % Allowed : 11.44 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.28 (0.13), residues: 4020 helix: 2.10 (0.25), residues: 456 sheet: 0.39 (0.14), residues: 1287 loop : -0.29 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 13 TYR 0.049 0.002 TYR C 242 PHE 0.014 0.001 PHE C 365 TRP 0.029 0.002 TRP E 64 HIS 0.020 0.001 HIS K 139 Details of bonding type rmsd covalent geometry : bond 0.00660 (31908) covalent geometry : angle 0.60196 (43460) SS BOND : bond 0.00487 ( 57) SS BOND : angle 1.26592 ( 114) hydrogen bonds : bond 0.03517 ( 1066) hydrogen bonds : angle 5.23861 ( 2706) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 354 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8569 (p) REVERT: A 211 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8730 (mmtt) REVERT: A 212 ASP cc_start: 0.8414 (t0) cc_final: 0.7558 (p0) REVERT: A 276 MET cc_start: 0.8406 (ttm) cc_final: 0.8187 (ttm) REVERT: A 345 GLU cc_start: 0.8494 (mp0) cc_final: 0.8179 (mp0) REVERT: A 400 GLN cc_start: 0.7657 (pm20) cc_final: 0.6647 (tm-30) REVERT: B 128 SER cc_start: 0.8929 (m) cc_final: 0.8496 (p) REVERT: B 138 GLN cc_start: 0.7708 (pt0) cc_final: 0.7499 (pp30) REVERT: B 140 ASN cc_start: 0.8956 (m-40) cc_final: 0.8539 (m-40) REVERT: B 166 MET cc_start: 0.9023 (mmm) cc_final: 0.8822 (mmm) REVERT: B 264 ASN cc_start: 0.9472 (t0) cc_final: 0.9204 (t0) REVERT: B 338 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8758 (p) REVERT: C 2 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8410 (tp30) REVERT: C 72 ASN cc_start: 0.9063 (t0) cc_final: 0.8722 (t0) REVERT: C 79 LYS cc_start: 0.8785 (tttp) cc_final: 0.8393 (ttmt) REVERT: C 187 MET cc_start: 0.8964 (ttt) cc_final: 0.8742 (ttm) REVERT: C 212 ASP cc_start: 0.8449 (t0) cc_final: 0.8147 (p0) REVERT: C 311 ASP cc_start: 0.8290 (t0) cc_final: 0.8034 (t0) REVERT: D 72 ASN cc_start: 0.8359 (p0) cc_final: 0.7944 (p0) REVERT: D 132 LYS cc_start: 0.8538 (tttt) cc_final: 0.8236 (ttmm) REVERT: D 212 ASP cc_start: 0.8306 (t0) cc_final: 0.7414 (p0) REVERT: D 400 GLN cc_start: 0.7820 (pm20) cc_final: 0.7438 (pm20) REVERT: D 401 ASP cc_start: 0.7652 (m-30) cc_final: 0.7323 (m-30) REVERT: D 407 MET cc_start: 0.7686 (ppp) cc_final: 0.7125 (ppp) REVERT: E 195 GLN cc_start: 0.8240 (mt0) cc_final: 0.7442 (pm20) REVERT: E 247 GLU cc_start: 0.8738 (pm20) cc_final: 0.8481 (pt0) REVERT: E 403 THR cc_start: 0.7241 (m) cc_final: 0.6703 (p) REVERT: F 171 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8838 (tpp) REVERT: F 254 LYS cc_start: 0.8645 (mttt) cc_final: 0.8441 (mttm) REVERT: G 200 LYS cc_start: 0.8195 (ptmt) cc_final: 0.7978 (tttp) REVERT: G 361 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8514 (mt-10) REVERT: G 388 MET cc_start: 0.5698 (mmp) cc_final: 0.5229 (mtt) REVERT: G 394 ARG cc_start: 0.7094 (mtp180) cc_final: 0.6480 (ttp80) REVERT: H 193 ASN cc_start: 0.8871 (m-40) cc_final: 0.8383 (t0) REVERT: I 122 LYS cc_start: 0.7862 (pttt) cc_final: 0.7248 (tttm) REVERT: I 135 MET cc_start: 0.6952 (mtt) cc_final: 0.5963 (mpp) REVERT: I 195 GLN cc_start: 0.7084 (tm-30) cc_final: 0.6765 (tm-30) REVERT: K 141 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8587 (ptmt) REVERT: K 151 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8129 (pttt) REVERT: K 209 LYS cc_start: 0.8799 (mmtm) cc_final: 0.8336 (ptpt) REVERT: L 115 PHE cc_start: 0.8512 (m-80) cc_final: 0.8231 (m-80) REVERT: L 161 ASP cc_start: 0.8547 (t0) cc_final: 0.8308 (t0) outliers start: 88 outliers final: 72 residues processed: 416 average time/residue: 0.1915 time to fit residues: 130.4473 Evaluate side-chains 423 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 346 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 27 MET Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 127 HIS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 247 GLU Chi-restraints excluded: chain G residue 291 HIS Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 397 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain J residue 139 HIS Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 139 HIS Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 247 LYS Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 212 ASP Chi-restraints excluded: chain L residue 227 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 317 optimal weight: 9.9990 chunk 348 optimal weight: 30.0000 chunk 170 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 373 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 208 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 248 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 439 HIS ** F 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 HIS K 139 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.121097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.082880 restraints weight = 54652.539| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.51 r_work: 0.2928 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31965 Z= 0.099 Angle : 0.521 9.608 43574 Z= 0.273 Chirality : 0.044 0.169 4884 Planarity : 0.004 0.050 5616 Dihedral : 5.234 86.882 4368 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.51 % Rotamer: Outliers : 1.66 % Allowed : 12.60 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.47 (0.13), residues: 4020 helix: 2.33 (0.25), residues: 456 sheet: 0.47 (0.15), residues: 1284 loop : -0.14 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 200 TYR 0.021 0.001 TYR C 242 PHE 0.019 0.001 PHE K 115 TRP 0.031 0.001 TRP E 64 HIS 0.030 0.001 HIS K 139 Details of bonding type rmsd covalent geometry : bond 0.00220 (31908) covalent geometry : angle 0.52003 (43460) SS BOND : bond 0.00222 ( 57) SS BOND : angle 0.91713 ( 114) hydrogen bonds : bond 0.03044 ( 1066) hydrogen bonds : angle 4.99197 ( 2706) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 360 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8715 (mmtt) REVERT: A 212 ASP cc_start: 0.8404 (t0) cc_final: 0.7586 (p0) REVERT: A 345 GLU cc_start: 0.8457 (mp0) cc_final: 0.8117 (mp0) REVERT: A 400 GLN cc_start: 0.7562 (pm20) cc_final: 0.6660 (tm-30) REVERT: B 128 SER cc_start: 0.8932 (m) cc_final: 0.8571 (p) REVERT: B 140 ASN cc_start: 0.8922 (m-40) cc_final: 0.8557 (m-40) REVERT: B 264 ASN cc_start: 0.9487 (t0) cc_final: 0.9187 (t0) REVERT: C 79 LYS cc_start: 0.8831 (tttp) cc_final: 0.8439 (ttmt) REVERT: C 212 ASP cc_start: 0.8433 (t0) cc_final: 0.8166 (p0) REVERT: C 311 ASP cc_start: 0.8211 (t0) cc_final: 0.7933 (t0) REVERT: D 72 ASN cc_start: 0.8326 (p0) cc_final: 0.7890 (p0) REVERT: D 132 LYS cc_start: 0.8557 (tttt) cc_final: 0.8254 (ttmm) REVERT: D 212 ASP cc_start: 0.8267 (t0) cc_final: 0.7376 (p0) REVERT: D 400 GLN cc_start: 0.7767 (pm20) cc_final: 0.7356 (pm20) REVERT: D 401 ASP cc_start: 0.7422 (m-30) cc_final: 0.7084 (m-30) REVERT: D 407 MET cc_start: 0.7603 (ppp) cc_final: 0.7022 (ppp) REVERT: E 195 GLN cc_start: 0.8231 (mt0) cc_final: 0.7508 (pm20) REVERT: E 247 GLU cc_start: 0.8643 (pm20) cc_final: 0.8417 (pt0) REVERT: E 403 THR cc_start: 0.7185 (m) cc_final: 0.6666 (p) REVERT: F 171 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8858 (tpp) REVERT: F 254 LYS cc_start: 0.8631 (mttt) cc_final: 0.8084 (mtpp) REVERT: G 354 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8335 (mt-10) REVERT: G 388 MET cc_start: 0.5650 (mmp) cc_final: 0.5235 (mtt) REVERT: G 394 ARG cc_start: 0.7094 (mtp180) cc_final: 0.6469 (ttp80) REVERT: H 193 ASN cc_start: 0.8815 (m-40) cc_final: 0.8365 (t0) REVERT: H 201 CYS cc_start: 0.6641 (OUTLIER) cc_final: 0.6189 (p) REVERT: I 122 LYS cc_start: 0.7825 (pttt) cc_final: 0.7134 (tttm) REVERT: I 135 MET cc_start: 0.7032 (mtt) cc_final: 0.6018 (mpp) REVERT: I 195 GLN cc_start: 0.7103 (tm-30) cc_final: 0.6751 (tm-30) REVERT: J 215 ARG cc_start: 0.8147 (mtt-85) cc_final: 0.7937 (mmm-85) REVERT: K 135 MET cc_start: 0.5480 (mpp) cc_final: 0.4702 (mpp) REVERT: K 151 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8079 (pttt) REVERT: K 209 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8303 (ptpt) REVERT: L 115 PHE cc_start: 0.8541 (m-80) cc_final: 0.8267 (m-80) REVERT: L 155 LYS cc_start: 0.6830 (tttp) cc_final: 0.6455 (tttt) REVERT: L 161 ASP cc_start: 0.8633 (t0) cc_final: 0.8372 (t0) outliers start: 57 outliers final: 48 residues processed: 398 average time/residue: 0.1950 time to fit residues: 126.2836 Evaluate side-chains 395 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 345 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 247 GLU Chi-restraints excluded: chain G residue 291 HIS Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 291 HIS Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 397 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 139 HIS Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 202 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 299 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 363 optimal weight: 9.9990 chunk 373 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 355 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 191 optimal weight: 8.9990 chunk 362 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN B 138 GLN F 127 HIS K 139 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.116188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.076505 restraints weight = 55444.703| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.59 r_work: 0.2857 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 31965 Z= 0.284 Angle : 0.611 10.546 43574 Z= 0.318 Chirality : 0.048 0.193 4884 Planarity : 0.005 0.050 5616 Dihedral : 5.490 88.627 4366 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 1.93 % Allowed : 12.63 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.27 (0.13), residues: 4020 helix: 2.13 (0.25), residues: 457 sheet: 0.36 (0.14), residues: 1293 loop : -0.29 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 13 TYR 0.017 0.002 TYR H 358 PHE 0.015 0.001 PHE C 365 TRP 0.036 0.002 TRP E 64 HIS 0.024 0.001 HIS K 139 Details of bonding type rmsd covalent geometry : bond 0.00680 (31908) covalent geometry : angle 0.60847 (43460) SS BOND : bond 0.00464 ( 57) SS BOND : angle 1.23638 ( 114) hydrogen bonds : bond 0.03446 ( 1066) hydrogen bonds : angle 5.17756 ( 2706) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 353 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8572 (p) REVERT: A 211 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8734 (mmtt) REVERT: A 212 ASP cc_start: 0.8523 (t0) cc_final: 0.7614 (p0) REVERT: A 345 GLU cc_start: 0.8551 (mp0) cc_final: 0.8233 (mp0) REVERT: A 400 GLN cc_start: 0.7590 (pm20) cc_final: 0.6787 (tm-30) REVERT: B 128 SER cc_start: 0.8923 (m) cc_final: 0.8520 (p) REVERT: B 138 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6700 (pp30) REVERT: B 140 ASN cc_start: 0.8886 (m-40) cc_final: 0.8561 (m-40) REVERT: B 264 ASN cc_start: 0.9456 (t0) cc_final: 0.9199 (t0) REVERT: B 338 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8768 (p) REVERT: C 72 ASN cc_start: 0.9005 (t0) cc_final: 0.8792 (t0) REVERT: C 79 LYS cc_start: 0.8823 (tttp) cc_final: 0.8442 (ttmt) REVERT: C 212 ASP cc_start: 0.8448 (t0) cc_final: 0.8152 (p0) REVERT: C 311 ASP cc_start: 0.8259 (t0) cc_final: 0.7998 (t0) REVERT: C 364 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8328 (mm-30) REVERT: D 72 ASN cc_start: 0.8379 (p0) cc_final: 0.7947 (p0) REVERT: D 132 LYS cc_start: 0.8537 (tttt) cc_final: 0.8233 (ttmm) REVERT: D 212 ASP cc_start: 0.8299 (t0) cc_final: 0.7375 (p0) REVERT: D 400 GLN cc_start: 0.7801 (pm20) cc_final: 0.7417 (pm20) REVERT: D 401 ASP cc_start: 0.7483 (m-30) cc_final: 0.7167 (m-30) REVERT: D 407 MET cc_start: 0.7704 (ppp) cc_final: 0.7228 (ppp) REVERT: E 195 GLN cc_start: 0.8334 (mt0) cc_final: 0.7831 (mt0) REVERT: E 247 GLU cc_start: 0.8724 (pm20) cc_final: 0.8486 (pt0) REVERT: E 403 THR cc_start: 0.7337 (m) cc_final: 0.6776 (p) REVERT: F 171 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8843 (tpp) REVERT: F 254 LYS cc_start: 0.8640 (mttt) cc_final: 0.8117 (mtpp) REVERT: G 388 MET cc_start: 0.5771 (mmp) cc_final: 0.5310 (mtt) REVERT: G 394 ARG cc_start: 0.7168 (mtp180) cc_final: 0.6521 (ttp80) REVERT: H 193 ASN cc_start: 0.8839 (m-40) cc_final: 0.8376 (t0) REVERT: H 201 CYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6150 (p) REVERT: I 122 LYS cc_start: 0.7953 (pttt) cc_final: 0.7288 (tttm) REVERT: I 135 MET cc_start: 0.6925 (mtt) cc_final: 0.5918 (mpp) REVERT: I 195 GLN cc_start: 0.7116 (tm-30) cc_final: 0.6745 (tm-30) REVERT: J 178 PHE cc_start: 0.7763 (t80) cc_final: 0.7406 (t80) REVERT: K 151 LYS cc_start: 0.8487 (ttmt) cc_final: 0.7963 (pttt) REVERT: K 209 LYS cc_start: 0.8746 (mmtm) cc_final: 0.8388 (ptpt) REVERT: L 115 PHE cc_start: 0.8528 (m-80) cc_final: 0.7885 (m-80) REVERT: L 126 TYR cc_start: 0.8737 (m-80) cc_final: 0.8246 (m-80) REVERT: L 155 LYS cc_start: 0.6815 (tttp) cc_final: 0.6470 (tttt) REVERT: L 161 ASP cc_start: 0.8558 (t0) cc_final: 0.8289 (t0) outliers start: 66 outliers final: 51 residues processed: 400 average time/residue: 0.1904 time to fit residues: 124.0987 Evaluate side-chains 402 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 346 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 127 HIS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 247 GLU Chi-restraints excluded: chain G residue 291 HIS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 397 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 139 HIS Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 191 optimal weight: 9.9990 chunk 361 optimal weight: 9.9990 chunk 152 optimal weight: 0.5980 chunk 325 optimal weight: 7.9990 chunk 313 optimal weight: 7.9990 chunk 306 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 327 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN F 127 HIS J 146 ASN K 139 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.120380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.080898 restraints weight = 55126.458| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.60 r_work: 0.2890 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31965 Z= 0.143 Angle : 0.551 10.139 43574 Z= 0.286 Chirality : 0.045 0.188 4884 Planarity : 0.004 0.050 5616 Dihedral : 5.337 88.960 4366 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 1.78 % Allowed : 12.78 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.30 (0.13), residues: 4020 helix: 2.16 (0.25), residues: 463 sheet: 0.35 (0.14), residues: 1315 loop : -0.25 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 200 TYR 0.019 0.001 TYR B 137 PHE 0.022 0.001 PHE K 115 TRP 0.038 0.001 TRP E 64 HIS 0.015 0.001 HIS K 139 Details of bonding type rmsd covalent geometry : bond 0.00336 (31908) covalent geometry : angle 0.54749 (43460) SS BOND : bond 0.00296 ( 57) SS BOND : angle 1.26219 ( 114) hydrogen bonds : bond 0.03131 ( 1066) hydrogen bonds : angle 5.04997 ( 2706) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 345 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8519 (p) REVERT: A 211 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8775 (mmtt) REVERT: A 212 ASP cc_start: 0.8566 (t0) cc_final: 0.7734 (p0) REVERT: A 345 GLU cc_start: 0.8540 (mp0) cc_final: 0.8209 (mp0) REVERT: A 400 GLN cc_start: 0.7534 (pm20) cc_final: 0.6655 (tm-30) REVERT: B 128 SER cc_start: 0.8953 (m) cc_final: 0.8483 (p) REVERT: B 264 ASN cc_start: 0.9495 (t0) cc_final: 0.9217 (t0) REVERT: B 338 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8621 (p) REVERT: C 79 LYS cc_start: 0.8783 (tttp) cc_final: 0.8390 (ttmt) REVERT: C 166 MET cc_start: 0.9126 (mmt) cc_final: 0.8610 (mmp) REVERT: C 212 ASP cc_start: 0.8454 (t0) cc_final: 0.8151 (p0) REVERT: C 311 ASP cc_start: 0.8191 (t0) cc_final: 0.7947 (t0) REVERT: D 72 ASN cc_start: 0.8375 (p0) cc_final: 0.7940 (p0) REVERT: D 132 LYS cc_start: 0.8479 (tttt) cc_final: 0.8170 (ttmm) REVERT: D 212 ASP cc_start: 0.8258 (t0) cc_final: 0.7341 (p0) REVERT: D 400 GLN cc_start: 0.7743 (pm20) cc_final: 0.7347 (pm20) REVERT: D 401 ASP cc_start: 0.7448 (m-30) cc_final: 0.7125 (m-30) REVERT: D 407 MET cc_start: 0.7569 (ppp) cc_final: 0.7076 (ppp) REVERT: E 195 GLN cc_start: 0.8314 (mt0) cc_final: 0.7798 (mt0) REVERT: E 247 GLU cc_start: 0.8645 (pm20) cc_final: 0.8414 (pt0) REVERT: E 403 THR cc_start: 0.7200 (m) cc_final: 0.6622 (p) REVERT: F 171 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8842 (tpp) REVERT: F 254 LYS cc_start: 0.8587 (mttt) cc_final: 0.8034 (mtpp) REVERT: G 388 MET cc_start: 0.5675 (mmp) cc_final: 0.5225 (mtt) REVERT: G 394 ARG cc_start: 0.7081 (mtp180) cc_final: 0.6447 (ttp80) REVERT: H 193 ASN cc_start: 0.8853 (m-40) cc_final: 0.8384 (t0) REVERT: H 201 CYS cc_start: 0.6534 (OUTLIER) cc_final: 0.6056 (p) REVERT: I 122 LYS cc_start: 0.7920 (pttt) cc_final: 0.7257 (tttm) REVERT: I 135 MET cc_start: 0.6915 (mtt) cc_final: 0.5913 (mpp) REVERT: I 195 GLN cc_start: 0.7051 (tm-30) cc_final: 0.6691 (tm-30) REVERT: J 178 PHE cc_start: 0.7620 (t80) cc_final: 0.7341 (t80) REVERT: K 139 HIS cc_start: 0.8908 (OUTLIER) cc_final: 0.8659 (t-90) REVERT: K 151 LYS cc_start: 0.8461 (ttmt) cc_final: 0.7940 (pttt) REVERT: K 189 TRP cc_start: 0.7560 (p-90) cc_final: 0.7330 (p-90) REVERT: K 209 LYS cc_start: 0.8764 (mmtm) cc_final: 0.8368 (ptpt) REVERT: L 115 PHE cc_start: 0.8443 (m-80) cc_final: 0.8165 (m-80) REVERT: L 155 LYS cc_start: 0.6694 (tttp) cc_final: 0.6349 (tttt) REVERT: L 161 ASP cc_start: 0.8452 (t0) cc_final: 0.8180 (t0) outliers start: 61 outliers final: 49 residues processed: 389 average time/residue: 0.1815 time to fit residues: 115.7893 Evaluate side-chains 396 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 342 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 171 MET Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 394 ARG Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 247 GLU Chi-restraints excluded: chain G residue 291 HIS Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 201 CYS Chi-restraints excluded: chain H residue 291 HIS Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain H residue 397 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain K residue 139 HIS Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 247 LYS Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 212 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 213 optimal weight: 0.9990 chunk 287 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 372 optimal weight: 6.9990 chunk 395 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 352 optimal weight: 50.0000 chunk 391 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 HIS J 146 ASN K 139 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.077840 restraints weight = 55340.025| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.61 r_work: 0.2883 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31965 Z= 0.183 Angle : 0.557 10.340 43574 Z= 0.289 Chirality : 0.045 0.209 4884 Planarity : 0.004 0.051 5616 Dihedral : 5.323 89.798 4366 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.59 % Rotamer: Outliers : 1.87 % Allowed : 12.81 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.30 (0.13), residues: 4020 helix: 2.16 (0.25), residues: 463 sheet: 0.35 (0.14), residues: 1312 loop : -0.26 (0.13), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 119 TYR 0.020 0.001 TYR L 196 PHE 0.025 0.001 PHE K 115 TRP 0.037 0.001 TRP E 64 HIS 0.011 0.001 HIS K 139 Details of bonding type rmsd covalent geometry : bond 0.00436 (31908) covalent geometry : angle 0.55387 (43460) SS BOND : bond 0.00336 ( 57) SS BOND : angle 1.24964 ( 114) hydrogen bonds : bond 0.03166 ( 1066) hydrogen bonds : angle 5.03261 ( 2706) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11973.50 seconds wall clock time: 204 minutes 31.10 seconds (12271.10 seconds total)