Starting phenix.real_space_refine on Tue Sep 15 05:24:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6j6i_0688/09_2026/6j6i_0688.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j6i_0688/09_2026/6j6i_0688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6j6i_0688/09_2026/6j6i_0688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j6i_0688/09_2026/6j6i_0688.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6j6i_0688/09_2026/6j6i_0688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j6i_0688/09_2026/6j6i_0688.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6j6i_0688/09_2026/6j6i_0688.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6j6i_0688/09_2026/6j6i_0688.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 218 5.16 5 C 22747 2.51 5 N 6177 2.21 5 O 6833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35992 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1510 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain breaks: 3 Chain: "B" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2629 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "C" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6330 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 27, 'TRANS': 762} Chain breaks: 2 Chain: "F" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6330 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 27, 'TRANS': 762} Chain breaks: 2 Chain: "G" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6330 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 27, 'TRANS': 762} Chain breaks: 2 Chain: "L" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6330 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 27, 'TRANS': 762} Chain breaks: 2 Chain: "O" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 6330 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 27, 'TRANS': 762} Chain breaks: 2 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DTP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N BQL A 501 " occ=0.00 ... (24 atoms not shown) pdb=" P BQL A 501 " occ=0.00 Time building chain proxies: 8.11, per 1000 atoms: 0.23 Number of scatterers: 35992 At special positions: 0 Unit cell: (210.563, 173.469, 104.736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 218 16.00 P 17 15.00 O 6833 8.00 N 6177 7.00 C 22747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of additional links: simple=2, symmetry=0 Simple link: pdb=" C VAL A 252 " - pdb=" N BQL A 501 " Simple link: pdb=" N LYS A 255 " - pdb=" C BQO A 502 " Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.4 seconds 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8408 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 29 sheets defined 42.2% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.596A pdb=" N PHE A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 Processing helix chain 'A' and resid 264 through 270 Processing helix chain 'A' and resid 274 through 292 Processing helix chain 'A' and resid 336 through 349 Processing helix chain 'A' and resid 358 through 365 removed outlier: 3.532A pdb=" N VAL A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 39 removed outlier: 4.357A pdb=" N SER B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 removed outlier: 4.426A pdb=" N ILE B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 96 removed outlier: 3.599A pdb=" N ILE B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.647A pdb=" N TYR B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 161 through 182 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 247 through 264 removed outlier: 4.000A pdb=" N SER B 253 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 289 Processing helix chain 'B' and resid 307 through 322 removed outlier: 3.864A pdb=" N GLN B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'C' and resid 28 through 45 removed outlier: 4.383A pdb=" N LEU C 34 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS C 39 " --> pdb=" O GLN C 35 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 removed outlier: 5.606A pdb=" N GLU C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 76 removed outlier: 4.125A pdb=" N GLU C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 109 through 136 Proline residue: C 131 - end of helix removed outlier: 3.939A pdb=" N ILE C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 175 Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.511A pdb=" N SER C 180 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 205 through 212 removed outlier: 3.705A pdb=" N GLU C 209 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 237 removed outlier: 3.582A pdb=" N ILE C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 299 through 305 Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'C' and resid 341 through 343 No H-bonds generated for 'chain 'C' and resid 341 through 343' Processing helix chain 'C' and resid 344 through 356 removed outlier: 3.724A pdb=" N LYS C 356 " --> pdb=" O VAL C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 Processing helix chain 'C' and resid 375 through 385 removed outlier: 3.979A pdb=" N TRP C 379 " --> pdb=" O VAL C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 391 removed outlier: 3.819A pdb=" N LEU C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 Processing helix chain 'C' and resid 399 through 409 removed outlier: 4.189A pdb=" N SER C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 421 removed outlier: 3.637A pdb=" N THR C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'C' and resid 433 through 443 Processing helix chain 'C' and resid 454 through 467 Processing helix chain 'C' and resid 488 through 500 Processing helix chain 'C' and resid 548 through 556 removed outlier: 4.113A pdb=" N ALA C 552 " --> pdb=" O ASN C 548 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR C 556 " --> pdb=" O ALA C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 579 Processing helix chain 'C' and resid 678 through 683 Processing helix chain 'C' and resid 695 through 699 removed outlier: 3.526A pdb=" N GLN C 698 " --> pdb=" O ARG C 695 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 699 " --> pdb=" O GLY C 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 695 through 699' Processing helix chain 'C' and resid 725 through 733 removed outlier: 3.831A pdb=" N ILE C 729 " --> pdb=" O GLY C 725 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 733 " --> pdb=" O ILE C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 784 Processing helix chain 'C' and resid 808 through 815 Processing helix chain 'F' and resid 28 through 45 removed outlier: 4.384A pdb=" N LEU F 34 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS F 39 " --> pdb=" O GLN F 35 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 51 removed outlier: 5.606A pdb=" N GLU F 49 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 76 removed outlier: 4.125A pdb=" N GLU F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 80 Processing helix chain 'F' and resid 109 through 136 Proline residue: F 131 - end of helix removed outlier: 3.939A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 175 Processing helix chain 'F' and resid 176 through 180 removed outlier: 3.512A pdb=" N SER F 180 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 205 through 212 removed outlier: 3.706A pdb=" N GLU F 209 " --> pdb=" O ASP F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 237 removed outlier: 3.581A pdb=" N ILE F 229 " --> pdb=" O THR F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 256 Processing helix chain 'F' and resid 273 through 275 No H-bonds generated for 'chain 'F' and resid 273 through 275' Processing helix chain 'F' and resid 276 through 281 Processing helix chain 'F' and resid 299 through 305 Processing helix chain 'F' and resid 319 through 332 Processing helix chain 'F' and resid 341 through 343 No H-bonds generated for 'chain 'F' and resid 341 through 343' Processing helix chain 'F' and resid 344 through 356 removed outlier: 3.724A pdb=" N LYS F 356 " --> pdb=" O VAL F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 370 Processing helix chain 'F' and resid 375 through 385 removed outlier: 3.978A pdb=" N TRP F 379 " --> pdb=" O VAL F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 391 removed outlier: 3.819A pdb=" N LEU F 390 " --> pdb=" O PHE F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 397 Processing helix chain 'F' and resid 399 through 409 removed outlier: 4.189A pdb=" N SER F 407 " --> pdb=" O SER F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 421 removed outlier: 3.636A pdb=" N THR F 421 " --> pdb=" O SER F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 424 No H-bonds generated for 'chain 'F' and resid 422 through 424' Processing helix chain 'F' and resid 433 through 443 Processing helix chain 'F' and resid 454 through 467 Processing helix chain 'F' and resid 488 through 500 Processing helix chain 'F' and resid 548 through 556 removed outlier: 4.113A pdb=" N ALA F 552 " --> pdb=" O ASN F 548 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR F 556 " --> pdb=" O ALA F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 579 Processing helix chain 'F' and resid 678 through 683 Processing helix chain 'F' and resid 695 through 699 removed outlier: 3.527A pdb=" N GLN F 698 " --> pdb=" O ARG F 695 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE F 699 " --> pdb=" O GLY F 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 695 through 699' Processing helix chain 'F' and resid 725 through 733 removed outlier: 3.831A pdb=" N ILE F 729 " --> pdb=" O GLY F 725 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP F 733 " --> pdb=" O ILE F 729 " (cutoff:3.500A) Processing helix chain 'F' and resid 780 through 784 Processing helix chain 'F' and resid 808 through 815 Processing helix chain 'G' and resid 28 through 45 removed outlier: 4.383A pdb=" N LEU G 34 " --> pdb=" O GLN G 30 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS G 39 " --> pdb=" O GLN G 35 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 51 removed outlier: 5.605A pdb=" N GLU G 49 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 76 removed outlier: 4.125A pdb=" N GLU G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 80 Processing helix chain 'G' and resid 109 through 136 Proline residue: G 131 - end of helix removed outlier: 3.938A pdb=" N ILE G 136 " --> pdb=" O TYR G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 175 Processing helix chain 'G' and resid 176 through 180 removed outlier: 3.512A pdb=" N SER G 180 " --> pdb=" O SER G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 205 through 212 removed outlier: 3.706A pdb=" N GLU G 209 " --> pdb=" O ASP G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 237 removed outlier: 3.582A pdb=" N ILE G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 256 Processing helix chain 'G' and resid 273 through 275 No H-bonds generated for 'chain 'G' and resid 273 through 275' Processing helix chain 'G' and resid 276 through 281 Processing helix chain 'G' and resid 299 through 305 Processing helix chain 'G' and resid 319 through 332 Processing helix chain 'G' and resid 341 through 343 No H-bonds generated for 'chain 'G' and resid 341 through 343' Processing helix chain 'G' and resid 344 through 356 removed outlier: 3.724A pdb=" N LYS G 356 " --> pdb=" O VAL G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 370 Processing helix chain 'G' and resid 375 through 385 removed outlier: 3.978A pdb=" N TRP G 379 " --> pdb=" O VAL G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 391 removed outlier: 3.819A pdb=" N LEU G 390 " --> pdb=" O PHE G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 397 Processing helix chain 'G' and resid 399 through 409 removed outlier: 4.189A pdb=" N SER G 407 " --> pdb=" O SER G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 421 removed outlier: 3.637A pdb=" N THR G 421 " --> pdb=" O SER G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 422 through 424 No H-bonds generated for 'chain 'G' and resid 422 through 424' Processing helix chain 'G' and resid 433 through 443 Processing helix chain 'G' and resid 454 through 467 Processing helix chain 'G' and resid 488 through 500 Processing helix chain 'G' and resid 548 through 556 removed outlier: 4.112A pdb=" N ALA G 552 " --> pdb=" O ASN G 548 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR G 556 " --> pdb=" O ALA G 552 " (cutoff:3.500A) Processing helix chain 'G' and resid 574 through 579 Processing helix chain 'G' and resid 678 through 683 Processing helix chain 'G' and resid 695 through 699 removed outlier: 3.527A pdb=" N GLN G 698 " --> pdb=" O ARG G 695 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE G 699 " --> pdb=" O GLY G 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 695 through 699' Processing helix chain 'G' and resid 725 through 733 removed outlier: 3.831A pdb=" N ILE G 729 " --> pdb=" O GLY G 725 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP G 733 " --> pdb=" O ILE G 729 " (cutoff:3.500A) Processing helix chain 'G' and resid 780 through 784 Processing helix chain 'G' and resid 808 through 815 Processing helix chain 'L' and resid 28 through 45 removed outlier: 4.383A pdb=" N LEU L 34 " --> pdb=" O GLN L 30 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS L 39 " --> pdb=" O GLN L 35 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 51 removed outlier: 5.605A pdb=" N GLU L 49 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 76 removed outlier: 4.126A pdb=" N GLU L 67 " --> pdb=" O ALA L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 80 Processing helix chain 'L' and resid 109 through 136 Proline residue: L 131 - end of helix removed outlier: 3.939A pdb=" N ILE L 136 " --> pdb=" O TYR L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 175 Processing helix chain 'L' and resid 176 through 180 removed outlier: 3.512A pdb=" N SER L 180 " --> pdb=" O SER L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 194 through 204 Processing helix chain 'L' and resid 205 through 212 removed outlier: 3.705A pdb=" N GLU L 209 " --> pdb=" O ASP L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 237 removed outlier: 3.582A pdb=" N ILE L 229 " --> pdb=" O THR L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 256 Processing helix chain 'L' and resid 273 through 275 No H-bonds generated for 'chain 'L' and resid 273 through 275' Processing helix chain 'L' and resid 276 through 281 Processing helix chain 'L' and resid 299 through 305 Processing helix chain 'L' and resid 319 through 332 Processing helix chain 'L' and resid 341 through 343 No H-bonds generated for 'chain 'L' and resid 341 through 343' Processing helix chain 'L' and resid 344 through 356 removed outlier: 3.724A pdb=" N LYS L 356 " --> pdb=" O VAL L 352 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 370 Processing helix chain 'L' and resid 375 through 385 removed outlier: 3.978A pdb=" N TRP L 379 " --> pdb=" O VAL L 375 " (cutoff:3.500A) Processing helix chain 'L' and resid 386 through 391 removed outlier: 3.819A pdb=" N LEU L 390 " --> pdb=" O PHE L 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 392 through 397 Processing helix chain 'L' and resid 399 through 409 removed outlier: 4.189A pdb=" N SER L 407 " --> pdb=" O SER L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 421 removed outlier: 3.637A pdb=" N THR L 421 " --> pdb=" O SER L 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 422 through 424 No H-bonds generated for 'chain 'L' and resid 422 through 424' Processing helix chain 'L' and resid 433 through 443 Processing helix chain 'L' and resid 454 through 467 Processing helix chain 'L' and resid 488 through 500 Processing helix chain 'L' and resid 548 through 556 removed outlier: 4.114A pdb=" N ALA L 552 " --> pdb=" O ASN L 548 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR L 556 " --> pdb=" O ALA L 552 " (cutoff:3.500A) Processing helix chain 'L' and resid 574 through 579 Processing helix chain 'L' and resid 678 through 683 Processing helix chain 'L' and resid 695 through 699 removed outlier: 3.527A pdb=" N GLN L 698 " --> pdb=" O ARG L 695 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE L 699 " --> pdb=" O GLY L 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 695 through 699' Processing helix chain 'L' and resid 725 through 733 removed outlier: 3.831A pdb=" N ILE L 729 " --> pdb=" O GLY L 725 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP L 733 " --> pdb=" O ILE L 729 " (cutoff:3.500A) Processing helix chain 'L' and resid 780 through 784 Processing helix chain 'L' and resid 808 through 815 Processing helix chain 'O' and resid 28 through 45 removed outlier: 4.383A pdb=" N LEU O 34 " --> pdb=" O GLN O 30 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS O 39 " --> pdb=" O GLN O 35 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER O 43 " --> pdb=" O LYS O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 51 removed outlier: 5.605A pdb=" N GLU O 49 " --> pdb=" O LYS O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 76 removed outlier: 4.125A pdb=" N GLU O 67 " --> pdb=" O ALA O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 80 Processing helix chain 'O' and resid 109 through 136 Proline residue: O 131 - end of helix removed outlier: 3.939A pdb=" N ILE O 136 " --> pdb=" O TYR O 132 " (cutoff:3.500A) Processing helix chain 'O' and resid 163 through 175 Processing helix chain 'O' and resid 176 through 180 removed outlier: 3.512A pdb=" N SER O 180 " --> pdb=" O SER O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 204 Processing helix chain 'O' and resid 205 through 212 removed outlier: 3.706A pdb=" N GLU O 209 " --> pdb=" O ASP O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 237 removed outlier: 3.581A pdb=" N ILE O 229 " --> pdb=" O THR O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 245 through 256 Processing helix chain 'O' and resid 273 through 275 No H-bonds generated for 'chain 'O' and resid 273 through 275' Processing helix chain 'O' and resid 276 through 281 Processing helix chain 'O' and resid 299 through 305 Processing helix chain 'O' and resid 319 through 332 Processing helix chain 'O' and resid 341 through 343 No H-bonds generated for 'chain 'O' and resid 341 through 343' Processing helix chain 'O' and resid 344 through 356 removed outlier: 3.724A pdb=" N LYS O 356 " --> pdb=" O VAL O 352 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 370 Processing helix chain 'O' and resid 375 through 385 removed outlier: 3.979A pdb=" N TRP O 379 " --> pdb=" O VAL O 375 " (cutoff:3.500A) Processing helix chain 'O' and resid 386 through 391 removed outlier: 3.819A pdb=" N LEU O 390 " --> pdb=" O PHE O 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 397 Processing helix chain 'O' and resid 399 through 409 removed outlier: 4.189A pdb=" N SER O 407 " --> pdb=" O SER O 403 " (cutoff:3.500A) Processing helix chain 'O' and resid 412 through 421 removed outlier: 3.636A pdb=" N THR O 421 " --> pdb=" O SER O 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 422 through 424 No H-bonds generated for 'chain 'O' and resid 422 through 424' Processing helix chain 'O' and resid 433 through 443 Processing helix chain 'O' and resid 454 through 467 Processing helix chain 'O' and resid 488 through 500 Processing helix chain 'O' and resid 548 through 556 removed outlier: 4.113A pdb=" N ALA O 552 " --> pdb=" O ASN O 548 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR O 556 " --> pdb=" O ALA O 552 " (cutoff:3.500A) Processing helix chain 'O' and resid 574 through 579 Processing helix chain 'O' and resid 678 through 683 Processing helix chain 'O' and resid 695 through 699 removed outlier: 3.527A pdb=" N GLN O 698 " --> pdb=" O ARG O 695 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE O 699 " --> pdb=" O GLY O 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 695 through 699' Processing helix chain 'O' and resid 725 through 733 removed outlier: 3.831A pdb=" N ILE O 729 " --> pdb=" O GLY O 725 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP O 733 " --> pdb=" O ILE O 729 " (cutoff:3.500A) Processing helix chain 'O' and resid 780 through 784 Processing helix chain 'O' and resid 808 through 815 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.833A pdb=" N GLY A 175 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.513A pdb=" N TRP B 74 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLN B 68 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR B 72 " --> pdb=" O GLN B 68 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 125 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU B 138 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU B 123 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 142 through 144 removed outlier: 4.121A pdb=" N LEU B 199 " --> pdb=" O HIS B 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 187 through 188 removed outlier: 3.701A pdb=" N ILE B 214 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 214 through 219 removed outlier: 6.337A pdb=" N ARG C 214 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL C 265 " --> pdb=" O ARG C 214 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE C 216 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASP C 267 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C 218 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL C 269 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU C 183 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 294 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET C 185 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N THR C 296 " --> pdb=" O MET C 185 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE C 187 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N HIS C 313 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA C 186 " --> pdb=" O HIS C 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 431 through 432 removed outlier: 7.188A pdb=" N ILE C 482 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LYS C 476 " --> pdb=" O ILE C 482 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR C 484 " --> pdb=" O VAL C 474 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 514 through 517 removed outlier: 3.501A pdb=" N SER C 537 " --> pdb=" O ASP C 565 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 592 " --> pdb=" O LEU C 564 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 545 through 546 removed outlier: 6.881A pdb=" N ASN C 545 " --> pdb=" O ILE C 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 614 through 616 removed outlier: 7.017A pdb=" N LEU C 663 " --> pdb=" O GLY C 690 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N SER C 692 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU C 744 " --> pdb=" O SER C 770 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 796 " --> pdb=" O THR C 822 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ASN C 824 " --> pdb=" O LEU C 796 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N LEU C 798 " --> pdb=" O ASN C 824 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 214 through 219 removed outlier: 6.338A pdb=" N ARG F 214 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL F 265 " --> pdb=" O ARG F 214 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE F 216 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP F 267 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL F 218 " --> pdb=" O ASP F 267 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL F 269 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU F 183 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL F 294 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET F 185 " --> pdb=" O VAL F 294 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N THR F 296 " --> pdb=" O MET F 185 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE F 187 " --> pdb=" O THR F 296 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N HIS F 313 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA F 186 " --> pdb=" O HIS F 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 431 through 432 removed outlier: 7.187A pdb=" N ILE F 482 " --> pdb=" O LYS F 476 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LYS F 476 " --> pdb=" O ILE F 482 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR F 484 " --> pdb=" O VAL F 474 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 514 through 517 removed outlier: 3.500A pdb=" N SER F 537 " --> pdb=" O ASP F 565 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER F 592 " --> pdb=" O LEU F 564 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 545 through 546 removed outlier: 6.881A pdb=" N ASN F 545 " --> pdb=" O ILE F 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 614 through 616 removed outlier: 7.017A pdb=" N LEU F 663 " --> pdb=" O GLY F 690 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER F 692 " --> pdb=" O LEU F 663 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU F 744 " --> pdb=" O SER F 770 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU F 796 " --> pdb=" O THR F 822 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ASN F 824 " --> pdb=" O LEU F 796 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N LEU F 798 " --> pdb=" O ASN F 824 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 214 through 219 removed outlier: 6.337A pdb=" N ARG G 214 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL G 265 " --> pdb=" O ARG G 214 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE G 216 " --> pdb=" O VAL G 265 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASP G 267 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL G 218 " --> pdb=" O ASP G 267 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL G 269 " --> pdb=" O VAL G 218 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU G 183 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL G 294 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N MET G 185 " --> pdb=" O VAL G 294 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR G 296 " --> pdb=" O MET G 185 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE G 187 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N HIS G 313 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA G 186 " --> pdb=" O HIS G 313 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 431 through 432 removed outlier: 7.187A pdb=" N ILE G 482 " --> pdb=" O LYS G 476 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LYS G 476 " --> pdb=" O ILE G 482 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N THR G 484 " --> pdb=" O VAL G 474 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 514 through 517 removed outlier: 3.638A pdb=" N SER G 592 " --> pdb=" O LEU G 564 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 545 through 546 removed outlier: 6.880A pdb=" N ASN G 545 " --> pdb=" O ILE G 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 614 through 616 removed outlier: 7.016A pdb=" N LEU G 663 " --> pdb=" O GLY G 690 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER G 692 " --> pdb=" O LEU G 663 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU G 744 " --> pdb=" O SER G 770 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU G 796 " --> pdb=" O THR G 822 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ASN G 824 " --> pdb=" O LEU G 796 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N LEU G 798 " --> pdb=" O ASN G 824 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 214 through 219 removed outlier: 6.338A pdb=" N ARG L 214 " --> pdb=" O LEU L 263 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL L 265 " --> pdb=" O ARG L 214 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE L 216 " --> pdb=" O VAL L 265 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP L 267 " --> pdb=" O ILE L 216 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL L 218 " --> pdb=" O ASP L 267 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL L 269 " --> pdb=" O VAL L 218 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU L 183 " --> pdb=" O VAL L 292 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL L 294 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET L 185 " --> pdb=" O VAL L 294 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N THR L 296 " --> pdb=" O MET L 185 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N PHE L 187 " --> pdb=" O THR L 296 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N HIS L 313 " --> pdb=" O ILE L 184 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA L 186 " --> pdb=" O HIS L 313 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 431 through 432 removed outlier: 7.188A pdb=" N ILE L 482 " --> pdb=" O LYS L 476 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LYS L 476 " --> pdb=" O ILE L 482 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR L 484 " --> pdb=" O VAL L 474 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 514 through 517 removed outlier: 3.638A pdb=" N SER L 592 " --> pdb=" O LEU L 564 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 545 through 546 removed outlier: 6.880A pdb=" N ASN L 545 " --> pdb=" O ILE L 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'L' and resid 614 through 616 removed outlier: 7.017A pdb=" N LEU L 663 " --> pdb=" O GLY L 690 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N SER L 692 " --> pdb=" O LEU L 663 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU L 744 " --> pdb=" O SER L 770 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU L 796 " --> pdb=" O THR L 822 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASN L 824 " --> pdb=" O LEU L 796 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N LEU L 798 " --> pdb=" O ASN L 824 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 214 through 219 removed outlier: 6.338A pdb=" N ARG O 214 " --> pdb=" O LEU O 263 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL O 265 " --> pdb=" O ARG O 214 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE O 216 " --> pdb=" O VAL O 265 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP O 267 " --> pdb=" O ILE O 216 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL O 218 " --> pdb=" O ASP O 267 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL O 269 " --> pdb=" O VAL O 218 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU O 183 " --> pdb=" O VAL O 292 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL O 294 " --> pdb=" O LEU O 183 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET O 185 " --> pdb=" O VAL O 294 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR O 296 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE O 187 " --> pdb=" O THR O 296 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N HIS O 313 " --> pdb=" O ILE O 184 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA O 186 " --> pdb=" O HIS O 313 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 431 through 432 removed outlier: 7.188A pdb=" N ILE O 482 " --> pdb=" O LYS O 476 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LYS O 476 " --> pdb=" O ILE O 482 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR O 484 " --> pdb=" O VAL O 474 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 514 through 517 removed outlier: 3.500A pdb=" N SER O 537 " --> pdb=" O ASP O 565 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER O 592 " --> pdb=" O LEU O 564 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 545 through 546 removed outlier: 6.881A pdb=" N ASN O 545 " --> pdb=" O ILE O 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'O' and resid 614 through 616 removed outlier: 7.017A pdb=" N LEU O 663 " --> pdb=" O GLY O 690 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N SER O 692 " --> pdb=" O LEU O 663 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU O 744 " --> pdb=" O SER O 770 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU O 796 " --> pdb=" O THR O 822 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASN O 824 " --> pdb=" O LEU O 796 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N LEU O 798 " --> pdb=" O ASN O 824 " (cutoff:3.500A) 1239 hydrogen bonds defined for protein. 3525 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.91 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6066 1.31 - 1.44: 9310 1.44 - 1.57: 20957 1.57 - 1.70: 31 1.70 - 1.82: 319 Bond restraints: 36683 Sorted by residual: bond pdb=" OP3 BQO A 502 " pdb=" P BQO A 502 " ideal model delta sigma weight residual 1.494 1.645 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C4 BQO A 502 " pdb=" C5 BQO A 502 " ideal model delta sigma weight residual 1.439 1.358 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C1' BQO A 502 " pdb=" N1 BQO A 502 " ideal model delta sigma weight residual 1.483 1.402 0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C1' BQO A 502 " pdb=" O4' BQO A 502 " ideal model delta sigma weight residual 1.390 1.466 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C2' BQO A 502 " pdb=" C3' BQO A 502 " ideal model delta sigma weight residual 1.531 1.463 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 36678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 48227 2.91 - 5.82: 1103 5.82 - 8.74: 192 8.74 - 11.65: 41 11.65 - 14.56: 19 Bond angle restraints: 49582 Sorted by residual: angle pdb=" PB DTP G 901 " pdb=" O3B DTP G 901 " pdb=" PG DTP G 901 " ideal model delta sigma weight residual 139.87 125.31 14.56 1.00e+00 1.00e+00 2.12e+02 angle pdb=" PA DTP F 901 " pdb=" O3A DTP F 901 " pdb=" PB DTP F 901 " ideal model delta sigma weight residual 136.83 122.70 14.13 1.00e+00 1.00e+00 2.00e+02 angle pdb=" PB DTP F 901 " pdb=" O3B DTP F 901 " pdb=" PG DTP F 901 " ideal model delta sigma weight residual 139.87 125.90 13.97 1.00e+00 1.00e+00 1.95e+02 angle pdb=" PA DTP C 901 " pdb=" O3A DTP C 901 " pdb=" PB DTP C 901 " ideal model delta sigma weight residual 136.83 123.58 13.25 1.00e+00 1.00e+00 1.76e+02 angle pdb=" PA DTP O 901 " pdb=" O3A DTP O 901 " pdb=" PB DTP O 901 " ideal model delta sigma weight residual 136.83 123.79 13.04 1.00e+00 1.00e+00 1.70e+02 ... (remaining 49577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 21302 22.41 - 44.81: 884 44.81 - 67.22: 58 67.22 - 89.63: 23 89.63 - 112.04: 4 Dihedral angle restraints: 22271 sinusoidal: 9293 harmonic: 12978 Sorted by residual: dihedral pdb=" CA PRO B 131 " pdb=" C PRO B 131 " pdb=" N PHE B 132 " pdb=" CA PHE B 132 " ideal model delta harmonic sigma weight residual -180.00 -104.42 -75.58 0 5.00e+00 4.00e-02 2.29e+02 dihedral pdb=" CA ASN G 506 " pdb=" C ASN G 506 " pdb=" N PRO G 507 " pdb=" CA PRO G 507 " ideal model delta harmonic sigma weight residual 180.00 -114.40 -65.60 0 5.00e+00 4.00e-02 1.72e+02 dihedral pdb=" CA ASN F 506 " pdb=" C ASN F 506 " pdb=" N PRO F 507 " pdb=" CA PRO F 507 " ideal model delta harmonic sigma weight residual -180.00 -114.41 -65.59 0 5.00e+00 4.00e-02 1.72e+02 ... (remaining 22268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4318 0.069 - 0.139: 1020 0.139 - 0.208: 188 0.208 - 0.277: 29 0.277 - 0.347: 8 Chirality restraints: 5563 Sorted by residual: chirality pdb=" CA THR B 231 " pdb=" N THR B 231 " pdb=" C THR B 231 " pdb=" CB THR B 231 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB ILE C 630 " pdb=" CA ILE C 630 " pdb=" CG1 ILE C 630 " pdb=" CG2 ILE C 630 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CB ILE B 296 " pdb=" CA ILE B 296 " pdb=" CG1 ILE B 296 " pdb=" CG2 ILE B 296 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 5560 not shown) Planarity restraints: 6285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 132 " -0.083 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO B 133 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 80 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLU B 80 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU B 80 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP B 81 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN O 506 " -0.045 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO O 507 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO O 507 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO O 507 " -0.038 5.00e-02 4.00e+02 ... (remaining 6282 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1063 2.69 - 3.24: 35011 3.24 - 3.79: 57197 3.79 - 4.35: 74129 4.35 - 4.90: 120810 Nonbonded interactions: 288210 Sorted by model distance: nonbonded pdb=" OE2 GLU F 472 " pdb=" NZ LYS F 486 " model vdw 2.132 3.120 nonbonded pdb=" OE2 GLU C 472 " pdb=" NZ LYS C 486 " model vdw 2.132 3.120 nonbonded pdb=" OE2 GLU G 472 " pdb=" NZ LYS G 486 " model vdw 2.132 3.120 nonbonded pdb=" OE2 GLU L 472 " pdb=" NZ LYS L 486 " model vdw 2.132 3.120 nonbonded pdb=" OE2 GLU O 472 " pdb=" NZ LYS O 486 " model vdw 2.133 3.120 ... (remaining 288205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'L' selection = chain 'O' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.150 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: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.050 Process input model: 34.960 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 : 0.007 0.151 36685 Z= 0.307 Angle : 1.139 14.562 49588 Z= 0.624 Chirality : 0.063 0.347 5563 Planarity : 0.008 0.125 6283 Dihedral : 11.880 112.035 13857 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.09 % Favored : 89.63 % Rotamer: Outliers : 0.72 % Allowed : 6.30 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.42 % 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: -4.37 (0.10), residues: 4428 helix: -2.55 (0.09), residues: 1642 sheet: -1.89 (0.21), residues: 508 loop : -3.50 (0.10), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 341 TYR 0.025 0.003 TYR F 256 PHE 0.030 0.003 PHE O 203 TRP 0.038 0.004 TRP B 162 HIS 0.017 0.003 HIS O 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.31 (36683) covalent geometry : angle 1.13860 / 0.62 (49582) hydrogen bonds : bond 0.16811 / 11.24 ( 1239) hydrogen bonds : angle 7.02702 / 4.88 ( 3525) link_TRANS : bond 0.00415 / 0.21 ( 2) link_TRANS : angle 0.46627 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 955 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLU cc_start: 0.8748 (mp0) cc_final: 0.8333 (mp0) REVERT: A 196 LYS cc_start: 0.8320 (mttt) cc_final: 0.7820 (mttp) REVERT: A 203 LYS cc_start: 0.8131 (tmmt) cc_final: 0.7852 (tmmt) REVERT: A 216 ILE cc_start: 0.8158 (mt) cc_final: 0.7868 (pt) REVERT: A 219 ASP cc_start: 0.7242 (t70) cc_final: 0.6901 (p0) REVERT: B 107 ASP cc_start: 0.8451 (t0) cc_final: 0.7993 (t0) REVERT: C 116 GLN cc_start: 0.9144 (tt0) cc_final: 0.8914 (tt0) REVERT: C 133 PHE cc_start: 0.8997 (m-80) cc_final: 0.8723 (m-80) REVERT: C 225 THR cc_start: 0.8807 (t) cc_final: 0.8025 (p) REVERT: C 335 ASN cc_start: 0.7623 (t0) cc_final: 0.7393 (t0) REVERT: C 405 GLN cc_start: 0.8379 (tt0) cc_final: 0.8116 (tt0) REVERT: C 409 ASP cc_start: 0.8332 (m-30) cc_final: 0.8055 (m-30) REVERT: C 561 LEU cc_start: 0.9264 (tm) cc_final: 0.9038 (tp) REVERT: C 602 PHE cc_start: 0.7583 (p90) cc_final: 0.7183 (p90) REVERT: C 612 LEU cc_start: 0.8704 (tt) cc_final: 0.8492 (tp) REVERT: C 722 ASP cc_start: 0.7201 (t0) cc_final: 0.6962 (t0) REVERT: F 125 ILE cc_start: 0.9199 (pp) cc_final: 0.8807 (mt) REVERT: F 237 LEU cc_start: 0.9004 (mt) cc_final: 0.8700 (mt) REVERT: F 515 LEU cc_start: 0.9152 (tm) cc_final: 0.8637 (tt) REVERT: F 763 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9056 (pp) REVERT: G 67 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7886 (tp30) REVERT: G 117 GLU cc_start: 0.8411 (pt0) cc_final: 0.8003 (pp20) REVERT: G 125 ILE cc_start: 0.9238 (pp) cc_final: 0.8988 (mt) REVERT: G 130 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7185 (tm-30) REVERT: G 225 THR cc_start: 0.8583 (t) cc_final: 0.7868 (p) REVERT: G 336 ASP cc_start: 0.7579 (t0) cc_final: 0.7352 (t0) REVERT: G 405 GLN cc_start: 0.8237 (tt0) cc_final: 0.7645 (tp40) REVERT: G 434 GLN cc_start: 0.8608 (tp-100) cc_final: 0.8275 (tp-100) REVERT: G 443 GLU cc_start: 0.8849 (pp20) cc_final: 0.8398 (pp20) REVERT: G 497 ASP cc_start: 0.8136 (t70) cc_final: 0.7643 (t70) REVERT: G 511 ASN cc_start: 0.8377 (t160) cc_final: 0.8070 (t0) REVERT: G 546 LYS cc_start: 0.7936 (tptp) cc_final: 0.7726 (mmtt) REVERT: G 703 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6673 (mt-10) REVERT: G 763 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8423 (pp) REVERT: G 779 MET cc_start: 0.7776 (mmt) cc_final: 0.7137 (pmm) REVERT: L 61 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8364 (pt) REVERT: L 67 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7734 (tp30) REVERT: L 184 ILE cc_start: 0.8605 (pt) cc_final: 0.8197 (mt) REVERT: L 225 THR cc_start: 0.8416 (t) cc_final: 0.7905 (p) REVERT: L 410 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7277 (mt-10) REVERT: L 490 MET cc_start: 0.8333 (mmm) cc_final: 0.8086 (mmp) REVERT: L 497 ASP cc_start: 0.8316 (t70) cc_final: 0.7864 (t0) REVERT: L 511 ASN cc_start: 0.8290 (t160) cc_final: 0.7833 (t0) REVERT: L 624 LYS cc_start: 0.8757 (mttp) cc_final: 0.8498 (mttt) REVERT: L 640 ASP cc_start: 0.8189 (t0) cc_final: 0.7852 (t0) REVERT: O 32 GLU cc_start: 0.8618 (pp20) cc_final: 0.8390 (pt0) REVERT: O 71 GLU cc_start: 0.8667 (tp30) cc_final: 0.8365 (tp30) REVERT: O 113 LYS cc_start: 0.9039 (mttt) cc_final: 0.8560 (mmtm) REVERT: O 116 GLN cc_start: 0.8985 (tt0) cc_final: 0.8563 (tt0) REVERT: O 120 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8167 (mt-10) REVERT: O 125 ILE cc_start: 0.9290 (pp) cc_final: 0.8979 (mt) REVERT: O 226 GLU cc_start: 0.8577 (mp0) cc_final: 0.8312 (mp0) REVERT: O 279 LYS cc_start: 0.8887 (mtmt) cc_final: 0.8678 (mtpt) REVERT: O 417 SER cc_start: 0.9079 (m) cc_final: 0.8744 (p) REVERT: O 567 SER cc_start: 0.8453 (m) cc_final: 0.8234 (p) REVERT: O 570 ILE cc_start: 0.9049 (mt) cc_final: 0.8826 (mm) REVERT: O 634 LYS cc_start: 0.8669 (pmtt) cc_final: 0.8469 (ptpp) outliers start: 29 outliers final: 6 residues processed: 975 average time/residue: 0.2454 time to fit residues: 374.5959 Evaluate side-chains 490 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 481 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 763 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 741 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 0.0060 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 232 ASN B 119 ASN B 154 ASN B 311 GLN C 288 GLN ** C 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN C 672 ASN C 673 ASN C 742 HIS C 747 GLN F 236 ASN F 273 ASN F 288 GLN F 322 ASN F 335 ASN F 377 HIS F 627 GLN F 672 ASN F 673 ASN F 742 HIS F 747 GLN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN G 288 GLN G 511 ASN G 587 HIS G 627 GLN G 672 ASN G 673 ASN G 742 HIS G 747 GLN L 288 GLN L 335 ASN L 399 ASN L 435 GLN L 511 ASN L 627 GLN L 672 ASN L 673 ASN L 742 HIS L 747 GLN O 30 GLN O 128 GLN ** O 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 288 GLN O 435 GLN O 625 GLN ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 672 ASN O 673 ASN O 742 HIS O 747 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.108206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.085832 restraints weight = 84903.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.088214 restraints weight = 48050.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.089831 restraints weight = 34042.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.090855 restraints weight = 27312.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.091525 restraints weight = 23763.142| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36685 Z= 0.153 Angle : 0.721 11.877 49588 Z= 0.377 Chirality : 0.047 0.206 5563 Planarity : 0.006 0.102 6283 Dihedral : 8.380 99.892 4905 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.10 % Favored : 90.61 % Rotamer: Outliers : 2.52 % Allowed : 11.57 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.11), residues: 4428 helix: -1.07 (0.12), residues: 1707 sheet: -1.74 (0.21), residues: 505 loop : -2.97 (0.12), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 308 TYR 0.023 0.002 TYR A 143 PHE 0.029 0.002 PHE O 748 TRP 0.024 0.002 TRP B 162 HIS 0.012 0.001 HIS C 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (36683) covalent geometry : angle 0.72074 / 0.38 (49582) hydrogen bonds : bond 0.04414 / 2.91 ( 1239) hydrogen bonds : angle 5.14471 / 3.58 ( 3525) link_TRANS : bond 0.00185 / 0.09 ( 2) link_TRANS : angle 0.72070 / 0.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 596 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 TYR cc_start: 0.8524 (p90) cc_final: 0.8096 (p90) REVERT: A 278 ASP cc_start: 0.8968 (m-30) cc_final: 0.8331 (m-30) REVERT: B 171 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 195 MET cc_start: 0.8665 (mmt) cc_final: 0.8338 (mpp) REVERT: C 116 GLN cc_start: 0.8904 (tt0) cc_final: 0.8620 (tt0) REVERT: C 130 GLU cc_start: 0.8355 (tt0) cc_final: 0.8142 (tt0) REVERT: C 133 PHE cc_start: 0.8896 (m-80) cc_final: 0.8579 (m-80) REVERT: C 184 ILE cc_start: 0.8526 (pt) cc_final: 0.8306 (mt) REVERT: C 410 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6693 (tm-30) REVERT: C 428 ASP cc_start: 0.7430 (m-30) cc_final: 0.6932 (m-30) REVERT: C 615 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8287 (tm) REVERT: C 650 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: C 689 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9377 (tm) REVERT: C 722 ASP cc_start: 0.7530 (t0) cc_final: 0.7178 (t0) REVERT: F 130 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7769 (tm-30) REVERT: F 237 LEU cc_start: 0.9133 (mt) cc_final: 0.8866 (mt) REVERT: F 545 ASN cc_start: 0.6356 (m-40) cc_final: 0.6016 (m-40) REVERT: F 604 ARG cc_start: 0.7675 (tmm-80) cc_final: 0.7461 (ttp80) REVERT: F 648 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: F 687 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7244 (mtp85) REVERT: F 733 ASP cc_start: 0.8365 (m-30) cc_final: 0.8019 (t0) REVERT: F 763 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8882 (pp) REVERT: G 67 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7909 (tp30) REVERT: G 130 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7456 (tm-30) REVERT: G 237 LEU cc_start: 0.9434 (mt) cc_final: 0.9176 (tt) REVERT: G 266 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8359 (mtp) REVERT: G 405 GLN cc_start: 0.7969 (tt0) cc_final: 0.7619 (tp40) REVERT: G 434 GLN cc_start: 0.8428 (tp-100) cc_final: 0.8223 (tp-100) REVERT: G 443 GLU cc_start: 0.8830 (pp20) cc_final: 0.8241 (pp20) REVERT: G 511 ASN cc_start: 0.8213 (t0) cc_final: 0.7871 (t0) REVERT: G 546 LYS cc_start: 0.8120 (tptp) cc_final: 0.7754 (mmtt) REVERT: G 779 MET cc_start: 0.7630 (mmt) cc_final: 0.7427 (pmm) REVERT: L 33 ASP cc_start: 0.8325 (p0) cc_final: 0.8051 (p0) REVERT: L 61 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8699 (tp) REVERT: L 230 MET cc_start: 0.8592 (mtm) cc_final: 0.8388 (mtm) REVERT: L 272 LYS cc_start: 0.8515 (tppt) cc_final: 0.8183 (tppt) REVERT: L 497 ASP cc_start: 0.8258 (t70) cc_final: 0.7940 (t0) REVERT: L 663 LEU cc_start: 0.9406 (tp) cc_final: 0.9105 (tt) REVERT: L 666 PHE cc_start: 0.7841 (t80) cc_final: 0.7527 (t80) REVERT: O 71 GLU cc_start: 0.8691 (tp30) cc_final: 0.8367 (tp30) REVERT: O 113 LYS cc_start: 0.9011 (mttt) cc_final: 0.8699 (mmtm) REVERT: O 116 GLN cc_start: 0.8940 (tt0) cc_final: 0.8606 (tt0) REVERT: O 120 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8190 (mt-10) REVERT: O 273 ASN cc_start: 0.8235 (t0) cc_final: 0.8025 (t0) REVERT: O 279 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8584 (mttt) REVERT: O 417 SER cc_start: 0.9096 (m) cc_final: 0.8682 (p) REVERT: O 455 THR cc_start: 0.7801 (p) cc_final: 0.7049 (m) REVERT: O 490 MET cc_start: 0.8388 (mmm) cc_final: 0.8187 (tpp) REVERT: O 515 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8508 (tp) REVERT: O 521 PHE cc_start: 0.6667 (m-80) cc_final: 0.6210 (m-80) REVERT: O 634 LYS cc_start: 0.8711 (pmtt) cc_final: 0.8468 (ptpp) outliers start: 102 outliers final: 40 residues processed: 668 average time/residue: 0.2100 time to fit residues: 230.7921 Evaluate side-chains 518 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 469 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 559 LYS Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 355 CYS Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 683 LEU Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 763 LEU Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 715 SER Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 587 HIS Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain O residue 30 GLN Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 435 GLN Chi-restraints excluded: chain O residue 515 LEU Chi-restraints excluded: chain O residue 590 CYS Chi-restraints excluded: chain O residue 660 LEU Chi-restraints excluded: chain O residue 741 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 308 optimal weight: 4.9990 chunk 242 optimal weight: 0.6980 chunk 205 optimal weight: 0.5980 chunk 15 optimal weight: 0.0370 chunk 286 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 219 optimal weight: 0.9990 chunk 253 optimal weight: 5.9990 chunk 285 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN A 151 ASN A 335 GLN A 343 ASN ** C 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN ** O 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.085843 restraints weight = 88656.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.088675 restraints weight = 46807.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.090136 restraints weight = 30414.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090152 restraints weight = 27286.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090247 restraints weight = 24818.072| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36685 Z= 0.126 Angle : 0.662 10.393 49588 Z= 0.344 Chirality : 0.046 0.177 5563 Planarity : 0.005 0.104 6283 Dihedral : 7.532 94.858 4897 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.28 % Favored : 90.58 % Rotamer: Outliers : 3.44 % Allowed : 12.80 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.12), residues: 4428 helix: -0.64 (0.12), residues: 1811 sheet: -1.56 (0.22), residues: 545 loop : -2.68 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 50 TYR 0.023 0.001 TYR A 143 PHE 0.027 0.001 PHE G 203 TRP 0.017 0.001 TRP B 162 HIS 0.007 0.001 HIS C 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (36683) covalent geometry : angle 0.66168 / 0.34 (49582) hydrogen bonds : bond 0.03653 / 2.41 ( 1239) hydrogen bonds : angle 4.73339 / 3.29 ( 3525) link_TRANS : bond 0.00110 / 0.05 ( 2) link_TRANS : angle 0.67737 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 577 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 HIS cc_start: 0.8455 (m-70) cc_final: 0.8178 (m-70) REVERT: A 226 LEU cc_start: 0.8051 (mt) cc_final: 0.7666 (mp) REVERT: A 359 MET cc_start: 0.7344 (mpp) cc_final: 0.6433 (mtt) REVERT: B 171 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7356 (mt-10) REVERT: B 195 MET cc_start: 0.8599 (mmt) cc_final: 0.8300 (mpp) REVERT: B 296 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.6752 (mp) REVERT: B 304 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7541 (tt) REVERT: C 116 GLN cc_start: 0.8927 (tt0) cc_final: 0.8332 (tt0) REVERT: C 130 GLU cc_start: 0.8318 (tt0) cc_final: 0.8071 (tt0) REVERT: C 133 PHE cc_start: 0.8894 (m-80) cc_final: 0.8632 (m-80) REVERT: C 615 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8356 (tm) REVERT: C 650 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.7011 (m-10) REVERT: C 689 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9352 (tm) REVERT: C 714 MET cc_start: 0.8354 (ttm) cc_final: 0.8095 (ttt) REVERT: C 722 ASP cc_start: 0.7381 (t0) cc_final: 0.6827 (t0) REVERT: F 130 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7726 (tm-30) REVERT: F 237 LEU cc_start: 0.9087 (mt) cc_final: 0.8816 (mt) REVERT: F 335 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7702 (t0) REVERT: F 427 GLU cc_start: 0.7946 (tp30) cc_final: 0.7662 (tp30) REVERT: F 648 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: F 687 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7366 (mtp85) REVERT: F 722 ASP cc_start: 0.7919 (m-30) cc_final: 0.7516 (p0) REVERT: F 830 GLU cc_start: 0.7467 (mp0) cc_final: 0.7155 (mp0) REVERT: G 47 ASP cc_start: 0.8241 (m-30) cc_final: 0.7857 (m-30) REVERT: G 67 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7856 (tp30) REVERT: G 130 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7428 (tm-30) REVERT: G 237 LEU cc_start: 0.9428 (mt) cc_final: 0.9205 (tt) REVERT: G 266 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8303 (mtp) REVERT: G 405 GLN cc_start: 0.7911 (tt0) cc_final: 0.7572 (tp40) REVERT: G 409 ASP cc_start: 0.8345 (m-30) cc_final: 0.8053 (m-30) REVERT: G 435 GLN cc_start: 0.7837 (tp40) cc_final: 0.7477 (tp-100) REVERT: G 443 GLU cc_start: 0.8727 (pp20) cc_final: 0.8178 (pp20) REVERT: G 511 ASN cc_start: 0.8209 (t0) cc_final: 0.7848 (t0) REVERT: G 546 LYS cc_start: 0.8168 (tptp) cc_final: 0.7851 (mmtt) REVERT: G 565 ASP cc_start: 0.8147 (p0) cc_final: 0.7641 (p0) REVERT: L 33 ASP cc_start: 0.8316 (p0) cc_final: 0.8049 (p0) REVERT: L 251 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8094 (mtm-85) REVERT: L 401 MET cc_start: 0.8133 (mmp) cc_final: 0.7640 (mmt) REVERT: L 497 ASP cc_start: 0.8283 (t70) cc_final: 0.8031 (t0) REVERT: L 666 PHE cc_start: 0.7888 (t80) cc_final: 0.7521 (t80) REVERT: O 71 GLU cc_start: 0.8670 (tp30) cc_final: 0.8375 (tp30) REVERT: O 75 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8909 (pt) REVERT: O 113 LYS cc_start: 0.9009 (mttt) cc_final: 0.8702 (mmtm) REVERT: O 116 GLN cc_start: 0.8881 (tt0) cc_final: 0.8422 (tt0) REVERT: O 120 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8094 (mt-10) REVERT: O 273 ASN cc_start: 0.8299 (t0) cc_final: 0.7907 (t0) REVERT: O 417 SER cc_start: 0.9061 (m) cc_final: 0.8719 (p) REVERT: O 521 PHE cc_start: 0.6613 (m-80) cc_final: 0.6080 (m-80) REVERT: O 634 LYS cc_start: 0.8756 (pmtt) cc_final: 0.8496 (ptpp) REVERT: O 640 ASP cc_start: 0.7843 (t0) cc_final: 0.7622 (t0) outliers start: 139 outliers final: 60 residues processed: 670 average time/residue: 0.2058 time to fit residues: 228.8656 Evaluate side-chains 536 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 465 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 650 PHE Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 689 LEU Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 647 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 746 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 570 ILE Chi-restraints excluded: chain O residue 660 LEU Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 804 LEU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 282 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 388 optimal weight: 0.7980 chunk 296 optimal weight: 1.9990 chunk 420 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 366 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 146 optimal weight: 0.4980 chunk 430 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 HIS A 335 GLN ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 587 HIS ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 30 GLN O 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.078458 restraints weight = 88379.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.081371 restraints weight = 49686.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.082858 restraints weight = 32033.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.082999 restraints weight = 28219.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.083095 restraints weight = 25308.267| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36685 Z= 0.150 Angle : 0.674 10.103 49588 Z= 0.346 Chirality : 0.047 0.178 5563 Planarity : 0.005 0.101 6283 Dihedral : 7.139 83.949 4893 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.39 % Favored : 90.40 % Rotamer: Outliers : 3.26 % Allowed : 14.31 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.12), residues: 4428 helix: -0.34 (0.12), residues: 1788 sheet: -1.43 (0.22), residues: 545 loop : -2.54 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 299 TYR 0.012 0.001 TYR B 105 PHE 0.030 0.001 PHE G 504 TRP 0.039 0.001 TRP L 757 HIS 0.008 0.001 HIS G 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (36683) covalent geometry : angle 0.67381 / 0.35 (49582) hydrogen bonds : bond 0.03723 / 2.44 ( 1239) hydrogen bonds : angle 4.60217 / 3.20 ( 3525) link_TRANS : bond 0.00184 / 0.09 ( 2) link_TRANS : angle 0.60248 / 0.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 500 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7922 (t80) cc_final: 0.7488 (t80) REVERT: A 226 LEU cc_start: 0.8170 (mt) cc_final: 0.7787 (mp) REVERT: A 359 MET cc_start: 0.7123 (mpp) cc_final: 0.6126 (ptp) REVERT: B 130 PHE cc_start: 0.7711 (m-10) cc_final: 0.7163 (m-10) REVERT: B 171 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7609 (mt-10) REVERT: B 195 MET cc_start: 0.8636 (mmt) cc_final: 0.8271 (mpp) REVERT: C 120 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7998 (mm-30) REVERT: C 130 GLU cc_start: 0.8300 (tt0) cc_final: 0.7944 (mt-10) REVERT: C 133 PHE cc_start: 0.8871 (m-80) cc_final: 0.8585 (m-80) REVERT: C 615 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8473 (tm) REVERT: C 650 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.7098 (m-10) REVERT: C 689 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9360 (tm) REVERT: C 714 MET cc_start: 0.8358 (ttm) cc_final: 0.8086 (ttt) REVERT: C 722 ASP cc_start: 0.7384 (t0) cc_final: 0.7030 (t0) REVERT: F 130 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7844 (tm-30) REVERT: F 428 ASP cc_start: 0.8034 (m-30) cc_final: 0.7808 (m-30) REVERT: F 648 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: F 656 SER cc_start: 0.8699 (m) cc_final: 0.8439 (p) REVERT: F 687 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7435 (mtp85) REVERT: F 722 ASP cc_start: 0.7964 (m-30) cc_final: 0.7528 (p0) REVERT: F 733 ASP cc_start: 0.8143 (m-30) cc_final: 0.7880 (t0) REVERT: F 830 GLU cc_start: 0.7582 (mp0) cc_final: 0.7169 (mp0) REVERT: G 67 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8140 (tp30) REVERT: G 130 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7483 (tm-30) REVERT: G 226 GLU cc_start: 0.8246 (mp0) cc_final: 0.7997 (mt-10) REVERT: G 237 LEU cc_start: 0.9431 (mt) cc_final: 0.9172 (tt) REVERT: G 266 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8321 (mtp) REVERT: G 405 GLN cc_start: 0.7949 (tt0) cc_final: 0.7465 (tp40) REVERT: G 435 GLN cc_start: 0.7783 (tp40) cc_final: 0.7392 (tp-100) REVERT: G 443 GLU cc_start: 0.8739 (pp20) cc_final: 0.8241 (pp20) REVERT: G 511 ASN cc_start: 0.8244 (t0) cc_final: 0.7911 (t0) REVERT: G 546 LYS cc_start: 0.8099 (tptp) cc_final: 0.7750 (mmtt) REVERT: G 565 ASP cc_start: 0.8073 (p0) cc_final: 0.7861 (p0) REVERT: G 763 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8691 (pp) REVERT: G 845 MET cc_start: 0.8110 (mmm) cc_final: 0.7907 (mmm) REVERT: L 33 ASP cc_start: 0.8401 (p0) cc_final: 0.8081 (p0) REVERT: L 251 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8125 (mtm-85) REVERT: L 401 MET cc_start: 0.8276 (mmp) cc_final: 0.7771 (mmt) REVERT: L 434 GLN cc_start: 0.8406 (tp-100) cc_final: 0.7988 (tp-100) REVERT: L 666 PHE cc_start: 0.7993 (t80) cc_final: 0.7569 (t80) REVERT: O 71 GLU cc_start: 0.8668 (tp30) cc_final: 0.8327 (tp30) REVERT: O 113 LYS cc_start: 0.8968 (mttt) cc_final: 0.8675 (mmtm) REVERT: O 120 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8137 (mt-10) REVERT: O 273 ASN cc_start: 0.8310 (t0) cc_final: 0.7873 (t0) REVERT: O 279 LYS cc_start: 0.8872 (mttt) cc_final: 0.8614 (ttmm) REVERT: O 335 ASN cc_start: 0.8122 (t0) cc_final: 0.7366 (t0) REVERT: O 417 SER cc_start: 0.9109 (m) cc_final: 0.8755 (p) REVERT: O 634 LYS cc_start: 0.8781 (pmtt) cc_final: 0.8509 (ptpp) REVERT: O 640 ASP cc_start: 0.7794 (t0) cc_final: 0.7532 (t0) REVERT: O 691 LEU cc_start: 0.8516 (mt) cc_final: 0.8232 (pp) outliers start: 132 outliers final: 79 residues processed: 594 average time/residue: 0.2112 time to fit residues: 207.3206 Evaluate side-chains 523 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 436 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 530 HIS Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 650 PHE Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 689 LEU Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 602 PHE Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 650 PHE Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 565 ASP Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 689 LEU Chi-restraints excluded: chain L residue 707 LEU Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 804 LEU Chi-restraints excluded: chain O residue 30 GLN Chi-restraints excluded: chain O residue 156 ASP Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 250 LEU Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 570 ILE Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 660 LEU Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 839 PHE Chi-restraints excluded: chain O residue 845 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 385 optimal weight: 4.9990 chunk 107 optimal weight: 0.0050 chunk 423 optimal weight: 1.9990 chunk 246 optimal weight: 0.5980 chunk 240 optimal weight: 0.9990 chunk 371 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 201 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 268 optimal weight: 0.6980 chunk 380 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 GLN ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 627 GLN ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN O 30 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.102723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.080370 restraints weight = 88108.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.083302 restraints weight = 48970.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.084792 restraints weight = 31813.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.084945 restraints weight = 28476.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085048 restraints weight = 25303.990| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36685 Z= 0.118 Angle : 0.649 11.393 49588 Z= 0.331 Chirality : 0.046 0.173 5563 Planarity : 0.005 0.097 6283 Dihedral : 6.768 77.382 4891 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.88 % Favored : 90.99 % Rotamer: Outliers : 3.41 % Allowed : 14.73 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.16 % 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: -1.91 (0.13), residues: 4428 helix: -0.15 (0.13), residues: 1788 sheet: -1.34 (0.23), residues: 545 loop : -2.28 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 604 TYR 0.025 0.001 TYR A 143 PHE 0.026 0.001 PHE A 282 TRP 0.038 0.001 TRP L 757 HIS 0.006 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (36683) covalent geometry : angle 0.64944 / 0.33 (49582) hydrogen bonds : bond 0.03352 / 2.21 ( 1239) hydrogen bonds : angle 4.48124 / 3.12 ( 3525) link_TRANS : bond 0.00106 / 0.05 ( 2) link_TRANS : angle 0.57877 / 0.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 504 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TRP cc_start: 0.5988 (t-100) cc_final: 0.5778 (t-100) REVERT: A 220 PHE cc_start: 0.7874 (t80) cc_final: 0.7433 (t80) REVERT: A 226 LEU cc_start: 0.8235 (mt) cc_final: 0.7909 (mp) REVERT: A 359 MET cc_start: 0.7207 (mpp) cc_final: 0.6221 (ptp) REVERT: B 130 PHE cc_start: 0.7598 (m-10) cc_final: 0.7315 (m-10) REVERT: B 195 MET cc_start: 0.8567 (mmt) cc_final: 0.7781 (mpp) REVERT: B 296 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6667 (mp) REVERT: B 304 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7594 (tt) REVERT: B 342 GLN cc_start: 0.8362 (pp30) cc_final: 0.7960 (pp30) REVERT: C 116 GLN cc_start: 0.8940 (tt0) cc_final: 0.8381 (tt0) REVERT: C 124 LYS cc_start: 0.9008 (tmmt) cc_final: 0.8687 (tptt) REVERT: C 130 GLU cc_start: 0.8343 (tt0) cc_final: 0.8040 (tt0) REVERT: C 650 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.7170 (m-10) REVERT: C 666 PHE cc_start: 0.8283 (t80) cc_final: 0.8000 (t80) REVERT: C 689 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9353 (tm) REVERT: C 714 MET cc_start: 0.8283 (ttm) cc_final: 0.7988 (ttt) REVERT: C 722 ASP cc_start: 0.7303 (t0) cc_final: 0.6946 (t0) REVERT: F 130 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7425 (tm-30) REVERT: F 428 ASP cc_start: 0.8080 (m-30) cc_final: 0.7874 (m-30) REVERT: F 641 MET cc_start: 0.8545 (mmt) cc_final: 0.7997 (mmt) REVERT: F 648 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: F 656 SER cc_start: 0.8611 (m) cc_final: 0.8399 (p) REVERT: F 687 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7362 (mtp85) REVERT: F 722 ASP cc_start: 0.8021 (m-30) cc_final: 0.7572 (p0) REVERT: F 830 GLU cc_start: 0.7571 (mp0) cc_final: 0.7157 (mp0) REVERT: G 67 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8126 (tp30) REVERT: G 130 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7476 (tm-30) REVERT: G 237 LEU cc_start: 0.9414 (mt) cc_final: 0.9185 (tt) REVERT: G 266 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8312 (mtp) REVERT: G 405 GLN cc_start: 0.7882 (tt0) cc_final: 0.7593 (tp40) REVERT: G 409 ASP cc_start: 0.8240 (m-30) cc_final: 0.7978 (m-30) REVERT: G 435 GLN cc_start: 0.7700 (tp40) cc_final: 0.7080 (mm-40) REVERT: G 443 GLU cc_start: 0.8684 (pp20) cc_final: 0.8142 (pp20) REVERT: G 511 ASN cc_start: 0.8175 (t0) cc_final: 0.7857 (t0) REVERT: G 546 LYS cc_start: 0.8080 (tptp) cc_final: 0.7735 (mmtt) REVERT: G 565 ASP cc_start: 0.8048 (p0) cc_final: 0.7617 (p0) REVERT: G 682 ASN cc_start: 0.8603 (m-40) cc_final: 0.8402 (t0) REVERT: G 763 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8676 (pp) REVERT: L 33 ASP cc_start: 0.8388 (p0) cc_final: 0.8071 (p0) REVERT: L 251 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7931 (mtm-85) REVERT: L 401 MET cc_start: 0.8178 (mmp) cc_final: 0.7677 (mmt) REVERT: L 634 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7980 (pptt) REVERT: L 666 PHE cc_start: 0.7883 (t80) cc_final: 0.7567 (t80) REVERT: O 71 GLU cc_start: 0.8631 (tp30) cc_final: 0.8290 (tp30) REVERT: O 113 LYS cc_start: 0.8887 (mttt) cc_final: 0.8658 (mmtm) REVERT: O 120 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8176 (mt-10) REVERT: O 184 ILE cc_start: 0.8444 (pt) cc_final: 0.8224 (mt) REVERT: O 273 ASN cc_start: 0.8293 (t0) cc_final: 0.7933 (t0) REVERT: O 279 LYS cc_start: 0.8879 (mttt) cc_final: 0.8610 (ttmm) REVERT: O 417 SER cc_start: 0.9059 (m) cc_final: 0.8696 (p) REVERT: O 634 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8554 (ptpp) REVERT: O 691 LEU cc_start: 0.8533 (mt) cc_final: 0.8298 (pp) outliers start: 138 outliers final: 79 residues processed: 603 average time/residue: 0.2120 time to fit residues: 212.5844 Evaluate side-chains 538 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 448 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain F residue 590 CYS Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 650 PHE Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 689 LEU Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 565 ASP Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 634 LYS Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 804 LEU Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 250 LEU Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 570 ILE Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 634 LYS Chi-restraints excluded: chain O residue 650 PHE Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 804 LEU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 313 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 225 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 309 optimal weight: 1.9990 chunk 364 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 292 optimal weight: 3.9990 chunk 407 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 387 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN A 347 GLN F 377 HIS G 385 HIS L 780 GLN O 30 GLN O 435 GLN ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 780 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.074343 restraints weight = 90050.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.076807 restraints weight = 51229.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.078443 restraints weight = 35984.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.079510 restraints weight = 28547.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.080218 restraints weight = 24575.723| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 36685 Z= 0.202 Angle : 0.715 12.621 49588 Z= 0.367 Chirality : 0.048 0.177 5563 Planarity : 0.005 0.100 6283 Dihedral : 6.886 68.266 4891 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.09 % Favored : 89.75 % Rotamer: Outliers : 3.71 % Allowed : 15.42 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.19 % 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: -1.93 (0.13), residues: 4428 helix: -0.09 (0.13), residues: 1728 sheet: -1.31 (0.22), residues: 535 loop : -2.32 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 604 TYR 0.022 0.002 TYR A 143 PHE 0.027 0.002 PHE G 203 TRP 0.041 0.002 TRP L 757 HIS 0.007 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (36683) covalent geometry : angle 0.71517 / 0.37 (49582) hydrogen bonds : bond 0.04120 / 2.70 ( 1239) hydrogen bonds : angle 4.60173 / 3.21 ( 3525) link_TRANS : bond 0.00278 / 0.13 ( 2) link_TRANS : angle 0.58074 / 0.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 460 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.7184 (mpp) cc_final: 0.6844 (mpp) REVERT: B 103 GLU cc_start: 0.8145 (mp0) cc_final: 0.7799 (mp0) REVERT: B 130 PHE cc_start: 0.8016 (m-10) cc_final: 0.7781 (m-10) REVERT: B 296 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.6945 (mp) REVERT: B 335 GLN cc_start: 0.8570 (mt0) cc_final: 0.8354 (mp10) REVERT: B 342 GLN cc_start: 0.8479 (pp30) cc_final: 0.8042 (pp30) REVERT: C 120 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7975 (mm-30) REVERT: C 401 MET cc_start: 0.8052 (mmm) cc_final: 0.7678 (mmt) REVERT: C 450 ASN cc_start: 0.6515 (p0) cc_final: 0.6314 (p0) REVERT: C 650 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7335 (m-10) REVERT: C 689 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9339 (tm) REVERT: C 714 MET cc_start: 0.8378 (ttm) cc_final: 0.8112 (ttt) REVERT: C 722 ASP cc_start: 0.7465 (t0) cc_final: 0.7092 (t0) REVERT: F 130 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7898 (tm-30) REVERT: F 272 LYS cc_start: 0.8804 (tptp) cc_final: 0.8374 (tptp) REVERT: F 273 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8117 (m110) REVERT: F 428 ASP cc_start: 0.8025 (m-30) cc_final: 0.7815 (m-30) REVERT: F 656 SER cc_start: 0.8603 (m) cc_final: 0.8396 (p) REVERT: F 687 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7485 (mtp85) REVERT: F 694 THR cc_start: 0.8048 (p) cc_final: 0.7723 (m) REVERT: F 722 ASP cc_start: 0.7934 (m-30) cc_final: 0.7553 (p0) REVERT: G 67 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8219 (tp30) REVERT: G 130 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7538 (tm-30) REVERT: G 237 LEU cc_start: 0.9427 (mt) cc_final: 0.9212 (tt) REVERT: G 266 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8436 (mtp) REVERT: G 385 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7991 (m90) REVERT: G 405 GLN cc_start: 0.8059 (tt0) cc_final: 0.7765 (tp40) REVERT: G 435 GLN cc_start: 0.7872 (tp40) cc_final: 0.7299 (mm-40) REVERT: G 497 ASP cc_start: 0.8011 (t70) cc_final: 0.7700 (t0) REVERT: G 511 ASN cc_start: 0.8212 (t0) cc_final: 0.7803 (t0) REVERT: G 546 LYS cc_start: 0.8146 (tptp) cc_final: 0.7821 (mmtt) REVERT: G 565 ASP cc_start: 0.8066 (p0) cc_final: 0.7809 (p0) REVERT: G 682 ASN cc_start: 0.8581 (m-40) cc_final: 0.8338 (t0) REVERT: G 763 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8741 (pp) REVERT: L 33 ASP cc_start: 0.8417 (p0) cc_final: 0.8066 (p0) REVERT: L 203 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7756 (p90) REVERT: L 251 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7953 (mtm-85) REVERT: L 388 ASP cc_start: 0.7468 (p0) cc_final: 0.7257 (p0) REVERT: L 506 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.7433 (t0) REVERT: L 634 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7947 (pmtt) REVERT: L 666 PHE cc_start: 0.7816 (t80) cc_final: 0.7494 (t80) REVERT: O 71 GLU cc_start: 0.8643 (tp30) cc_final: 0.8299 (tp30) REVERT: O 113 LYS cc_start: 0.8963 (mttt) cc_final: 0.8746 (mmtm) REVERT: O 116 GLN cc_start: 0.8944 (tt0) cc_final: 0.8387 (tt0) REVERT: O 120 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8214 (mt-10) REVERT: O 273 ASN cc_start: 0.8500 (t0) cc_final: 0.8066 (t0) REVERT: O 279 LYS cc_start: 0.8921 (mttt) cc_final: 0.8635 (ttmm) REVERT: O 417 SER cc_start: 0.9148 (m) cc_final: 0.8815 (p) REVERT: O 634 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8440 (ptpp) REVERT: O 691 LEU cc_start: 0.8522 (mt) cc_final: 0.8234 (pp) outliers start: 150 outliers final: 94 residues processed: 574 average time/residue: 0.2165 time to fit residues: 204.4229 Evaluate side-chains 528 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 421 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 602 PHE Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 590 CYS Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 689 LEU Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 385 HIS Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 602 PHE Chi-restraints excluded: chain G residue 614 ILE Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 506 ASN Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 565 ASP Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 634 LYS Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 804 LEU Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 435 GLN Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 570 ILE Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 634 LYS Chi-restraints excluded: chain O residue 650 PHE Chi-restraints excluded: chain O residue 654 ILE Chi-restraints excluded: chain O residue 699 ILE Chi-restraints excluded: chain O residue 713 LEU Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 804 LEU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 8 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 327 optimal weight: 3.9990 chunk 386 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 429 optimal weight: 0.0060 chunk 420 optimal weight: 4.9990 chunk 411 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 GLN C 611 ASN C 761 HIS G 385 HIS G 698 GLN ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.098239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.076443 restraints weight = 90530.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.078899 restraints weight = 51120.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.079949 restraints weight = 34536.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.080286 restraints weight = 30888.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.080324 restraints weight = 27706.502| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36685 Z= 0.152 Angle : 0.688 12.836 49588 Z= 0.348 Chirality : 0.047 0.242 5563 Planarity : 0.005 0.099 6283 Dihedral : 6.685 67.095 4891 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.03 % Favored : 90.79 % Rotamer: Outliers : 3.29 % Allowed : 16.49 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.21 % 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: -1.84 (0.13), residues: 4428 helix: -0.03 (0.13), residues: 1758 sheet: -1.31 (0.22), residues: 535 loop : -2.26 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 604 TYR 0.018 0.001 TYR A 143 PHE 0.024 0.001 PHE G 203 TRP 0.028 0.001 TRP L 757 HIS 0.008 0.001 HIS G 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (36683) covalent geometry : angle 0.68773 / 0.35 (49582) hydrogen bonds : bond 0.03679 / 2.41 ( 1239) hydrogen bonds : angle 4.49283 / 3.12 ( 3525) link_TRANS : bond 0.00172 / 0.08 ( 2) link_TRANS : angle 0.52917 / 0.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 471 time to evaluate : 1.089 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 359 MET cc_start: 0.7165 (mpp) cc_final: 0.6810 (mpp) REVERT: B 103 GLU cc_start: 0.8107 (mp0) cc_final: 0.7762 (mp0) REVERT: B 130 PHE cc_start: 0.7942 (m-10) cc_final: 0.7732 (m-10) REVERT: B 296 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6954 (mp) REVERT: B 304 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7650 (tt) REVERT: B 342 GLN cc_start: 0.8494 (pp30) cc_final: 0.8052 (pp30) REVERT: C 116 GLN cc_start: 0.8899 (tt0) cc_final: 0.8426 (tt0) REVERT: C 120 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7995 (mm-30) REVERT: C 203 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7164 (p90) REVERT: C 237 LEU cc_start: 0.9163 (tp) cc_final: 0.8852 (tt) REVERT: C 401 MET cc_start: 0.8139 (mmm) cc_final: 0.7795 (mmt) REVERT: C 650 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7434 (m-10) REVERT: C 689 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9327 (tm) REVERT: C 722 ASP cc_start: 0.7354 (t0) cc_final: 0.6980 (t0) REVERT: F 130 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7751 (tm-30) REVERT: F 272 LYS cc_start: 0.8836 (tptp) cc_final: 0.8425 (tptp) REVERT: F 273 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8039 (m110) REVERT: F 428 ASP cc_start: 0.8003 (m-30) cc_final: 0.7800 (m-30) REVERT: F 445 PHE cc_start: 0.9138 (m-10) cc_final: 0.8473 (m-10) REVERT: F 640 ASP cc_start: 0.8186 (t0) cc_final: 0.7749 (t0) REVERT: F 641 MET cc_start: 0.8558 (mmt) cc_final: 0.7982 (mmt) REVERT: F 656 SER cc_start: 0.8597 (m) cc_final: 0.8385 (p) REVERT: F 687 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7412 (mtp85) REVERT: F 714 MET cc_start: 0.8469 (ttm) cc_final: 0.8235 (ttm) REVERT: G 67 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8173 (tp30) REVERT: G 130 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7494 (tm-30) REVERT: G 237 LEU cc_start: 0.9427 (mt) cc_final: 0.9220 (tt) REVERT: G 266 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8430 (mtp) REVERT: G 385 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.8085 (m-70) REVERT: G 405 GLN cc_start: 0.8048 (tt0) cc_final: 0.7724 (tp40) REVERT: G 435 GLN cc_start: 0.7760 (tp40) cc_final: 0.7195 (mm-40) REVERT: G 443 GLU cc_start: 0.8770 (pp20) cc_final: 0.8160 (pp20) REVERT: G 497 ASP cc_start: 0.8005 (t70) cc_final: 0.7715 (t0) REVERT: G 511 ASN cc_start: 0.8256 (t0) cc_final: 0.7840 (t0) REVERT: G 546 LYS cc_start: 0.8135 (tptp) cc_final: 0.7785 (mmtt) REVERT: G 625 GLN cc_start: 0.7026 (tp40) cc_final: 0.6674 (tm-30) REVERT: G 682 ASN cc_start: 0.8552 (m-40) cc_final: 0.8321 (t0) REVERT: G 763 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8772 (pp) REVERT: L 33 ASP cc_start: 0.8397 (p0) cc_final: 0.8048 (p0) REVERT: L 39 LYS cc_start: 0.9492 (OUTLIER) cc_final: 0.9286 (tttm) REVERT: L 203 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7821 (p90) REVERT: L 251 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8001 (mtm-85) REVERT: L 374 HIS cc_start: 0.8361 (m-70) cc_final: 0.8096 (m170) REVERT: L 388 ASP cc_start: 0.7504 (p0) cc_final: 0.7164 (p0) REVERT: L 401 MET cc_start: 0.8141 (mmp) cc_final: 0.7571 (mmt) REVERT: L 434 GLN cc_start: 0.8470 (tp-100) cc_final: 0.8207 (tp-100) REVERT: L 634 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8003 (pptt) REVERT: L 666 PHE cc_start: 0.7803 (t80) cc_final: 0.7467 (t80) REVERT: O 71 GLU cc_start: 0.8628 (tp30) cc_final: 0.8269 (tp30) REVERT: O 113 LYS cc_start: 0.8972 (mttt) cc_final: 0.8733 (mmtm) REVERT: O 120 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8190 (mt-10) REVERT: O 279 LYS cc_start: 0.8931 (mttt) cc_final: 0.8642 (ttmm) REVERT: O 417 SER cc_start: 0.9117 (m) cc_final: 0.8799 (p) REVERT: O 427 GLU cc_start: 0.7780 (tp30) cc_final: 0.7408 (tp30) REVERT: O 634 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8379 (ptpp) REVERT: O 691 LEU cc_start: 0.8514 (mt) cc_final: 0.8246 (pp) outliers start: 133 outliers final: 95 residues processed: 571 average time/residue: 0.2106 time to fit residues: 197.9236 Evaluate side-chains 542 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 432 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 602 PHE Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 213 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 590 CYS Chi-restraints excluded: chain F residue 650 PHE Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 689 LEU Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 385 HIS Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 515 LEU Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 602 PHE Chi-restraints excluded: chain G residue 614 ILE Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 514 HIS Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 565 ASP Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 615 LEU Chi-restraints excluded: chain L residue 634 LYS Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 758 LEU Chi-restraints excluded: chain L residue 763 LEU Chi-restraints excluded: chain L residue 804 LEU Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 570 ILE Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 634 LYS Chi-restraints excluded: chain O residue 650 PHE Chi-restraints excluded: chain O residue 654 ILE Chi-restraints excluded: chain O residue 699 ILE Chi-restraints excluded: chain O residue 713 LEU Chi-restraints excluded: chain O residue 722 ASP Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 804 LEU Chi-restraints excluded: chain O residue 806 MET Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 108 optimal weight: 0.0980 chunk 303 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 283 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 214 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 369 optimal weight: 2.9990 chunk 386 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 GLN C 611 ASN F 377 HIS F 545 ASN G 385 HIS ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 435 GLN ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.076877 restraints weight = 89403.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.079445 restraints weight = 50948.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.081115 restraints weight = 35681.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.082246 restraints weight = 28334.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.083008 restraints weight = 24243.707| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36685 Z= 0.132 Angle : 0.678 12.775 49588 Z= 0.342 Chirality : 0.046 0.209 5563 Planarity : 0.005 0.097 6283 Dihedral : 6.491 62.795 4891 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.69 % Favored : 90.20 % Rotamer: Outliers : 3.34 % Allowed : 16.76 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.16 % 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: -1.77 (0.13), residues: 4428 helix: -0.02 (0.13), residues: 1764 sheet: -1.31 (0.23), residues: 510 loop : -2.17 (0.14), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 604 TYR 0.022 0.001 TYR A 143 PHE 0.022 0.001 PHE G 203 TRP 0.026 0.001 TRP L 757 HIS 0.022 0.001 HIS G 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (36683) covalent geometry : angle 0.67756 / 0.34 (49582) hydrogen bonds : bond 0.03460 / 2.27 ( 1239) hydrogen bonds : angle 4.43452 / 3.08 ( 3525) link_TRANS : bond 0.00137 / 0.07 ( 2) link_TRANS : angle 0.52503 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 479 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 MET cc_start: 0.7164 (mpp) cc_final: 0.6833 (mpp) REVERT: B 103 GLU cc_start: 0.8091 (mp0) cc_final: 0.7765 (mp0) REVERT: B 296 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.7000 (mp) REVERT: B 304 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7501 (tt) REVERT: B 342 GLN cc_start: 0.8468 (pp30) cc_final: 0.8044 (pp30) REVERT: C 116 GLN cc_start: 0.8909 (tt0) cc_final: 0.8398 (tt0) REVERT: C 120 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7972 (mm-30) REVERT: C 133 PHE cc_start: 0.8843 (m-80) cc_final: 0.8554 (m-80) REVERT: C 203 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7097 (p90) REVERT: C 237 LEU cc_start: 0.9075 (tp) cc_final: 0.8799 (tt) REVERT: C 401 MET cc_start: 0.8090 (mmm) cc_final: 0.7745 (mmt) REVERT: C 650 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7443 (m-10) REVERT: C 689 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9315 (tm) REVERT: C 722 ASP cc_start: 0.7332 (t0) cc_final: 0.6861 (t0) REVERT: F 130 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7772 (tm-30) REVERT: F 272 LYS cc_start: 0.8841 (tptp) cc_final: 0.8393 (tptp) REVERT: F 273 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.7958 (m110) REVERT: F 428 ASP cc_start: 0.7988 (m-30) cc_final: 0.7781 (m-30) REVERT: F 641 MET cc_start: 0.8524 (mmt) cc_final: 0.7925 (mmt) REVERT: F 656 SER cc_start: 0.8595 (m) cc_final: 0.8368 (p) REVERT: F 687 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7292 (mtp85) REVERT: F 714 MET cc_start: 0.8486 (ttm) cc_final: 0.8260 (ttm) REVERT: F 830 GLU cc_start: 0.7469 (mp0) cc_final: 0.7131 (mp0) REVERT: G 40 TYR cc_start: 0.8630 (m-80) cc_final: 0.8366 (m-80) REVERT: G 67 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8220 (tp30) REVERT: G 130 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7495 (tm-30) REVERT: G 237 LEU cc_start: 0.9418 (mt) cc_final: 0.9218 (tt) REVERT: G 266 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8437 (mtp) REVERT: G 405 GLN cc_start: 0.7960 (tt0) cc_final: 0.7664 (tp40) REVERT: G 443 GLU cc_start: 0.8762 (pp20) cc_final: 0.8258 (pp20) REVERT: G 511 ASN cc_start: 0.8152 (t0) cc_final: 0.7893 (t0) REVERT: G 546 LYS cc_start: 0.8183 (tptp) cc_final: 0.7834 (mmtt) REVERT: G 625 GLN cc_start: 0.7136 (tp40) cc_final: 0.6768 (tm-30) REVERT: G 763 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8749 (pp) REVERT: L 33 ASP cc_start: 0.8372 (p0) cc_final: 0.8046 (p0) REVERT: L 39 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9272 (tttm) REVERT: L 203 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7596 (p90) REVERT: L 251 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8014 (mtm-85) REVERT: L 374 HIS cc_start: 0.8326 (m-70) cc_final: 0.8091 (m170) REVERT: L 401 MET cc_start: 0.7940 (mmp) cc_final: 0.7356 (mmt) REVERT: L 434 GLN cc_start: 0.8401 (tp-100) cc_final: 0.8119 (tp-100) REVERT: L 567 SER cc_start: 0.8683 (p) cc_final: 0.8468 (p) REVERT: L 634 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7979 (pptt) REVERT: L 650 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.6242 (t80) REVERT: L 666 PHE cc_start: 0.7770 (t80) cc_final: 0.7563 (t80) REVERT: L 700 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6906 (tm-30) REVERT: L 779 MET cc_start: 0.7829 (mmm) cc_final: 0.7172 (mmm) REVERT: O 71 GLU cc_start: 0.8665 (tp30) cc_final: 0.8321 (tp30) REVERT: O 120 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8187 (mt-10) REVERT: O 279 LYS cc_start: 0.8908 (mttt) cc_final: 0.8590 (ttmm) REVERT: O 417 SER cc_start: 0.9089 (m) cc_final: 0.8749 (p) REVERT: O 427 GLU cc_start: 0.7897 (tp30) cc_final: 0.7272 (tp30) REVERT: O 428 ASP cc_start: 0.7819 (m-30) cc_final: 0.7197 (m-30) REVERT: O 521 PHE cc_start: 0.6423 (m-80) cc_final: 0.5988 (m-80) REVERT: O 634 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8441 (ptpp) REVERT: O 691 LEU cc_start: 0.8452 (mt) cc_final: 0.8236 (pp) outliers start: 135 outliers final: 92 residues processed: 579 average time/residue: 0.2134 time to fit residues: 204.0194 Evaluate side-chains 546 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 439 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 602 PHE Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 213 GLU Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 590 CYS Chi-restraints excluded: chain F residue 614 ILE Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 650 PHE Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 689 LEU Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 602 PHE Chi-restraints excluded: chain G residue 615 LEU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 514 HIS Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 615 LEU Chi-restraints excluded: chain L residue 634 LYS Chi-restraints excluded: chain L residue 650 PHE Chi-restraints excluded: chain L residue 689 LEU Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 758 LEU Chi-restraints excluded: chain L residue 763 LEU Chi-restraints excluded: chain L residue 794 GLU Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 570 ILE Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 634 LYS Chi-restraints excluded: chain O residue 650 PHE Chi-restraints excluded: chain O residue 654 ILE Chi-restraints excluded: chain O residue 699 ILE Chi-restraints excluded: chain O residue 713 LEU Chi-restraints excluded: chain O residue 722 ASP Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 804 LEU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 3 optimal weight: 0.0970 chunk 445 optimal weight: 0.2980 chunk 224 optimal weight: 0.9980 chunk 143 optimal weight: 0.0570 chunk 191 optimal weight: 8.9990 chunk 348 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 334 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 222 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 611 ASN F 545 ASN G 385 HIS ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.100724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.079011 restraints weight = 89542.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.082001 restraints weight = 47913.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.083247 restraints weight = 30999.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.083475 restraints weight = 27710.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.083515 restraints weight = 25014.182| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36685 Z= 0.119 Angle : 0.678 12.407 49588 Z= 0.340 Chirality : 0.046 0.204 5563 Planarity : 0.005 0.095 6283 Dihedral : 6.295 61.690 4891 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.90 % Favored : 91.01 % Rotamer: Outliers : 2.79 % Allowed : 17.89 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.14 % 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: -1.69 (0.13), residues: 4428 helix: 0.01 (0.13), residues: 1799 sheet: -1.27 (0.23), residues: 510 loop : -2.11 (0.14), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 604 TYR 0.020 0.001 TYR A 143 PHE 0.020 0.001 PHE G 203 TRP 0.057 0.001 TRP L 757 HIS 0.007 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (36683) covalent geometry : angle 0.67797 / 0.34 (49582) hydrogen bonds : bond 0.03261 / 2.13 ( 1239) hydrogen bonds : angle 4.35941 / 3.03 ( 3525) link_TRANS : bond 0.00088 / 0.04 ( 2) link_TRANS : angle 0.55153 / 0.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 489 time to evaluate : 1.263 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 172 MET cc_start: 0.6668 (mmp) cc_final: 0.6454 (tpp) REVERT: A 359 MET cc_start: 0.7146 (mpp) cc_final: 0.6823 (mpp) REVERT: B 130 PHE cc_start: 0.7698 (m-10) cc_final: 0.7403 (m-10) REVERT: B 296 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6975 (mp) REVERT: B 304 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7552 (tt) REVERT: B 342 GLN cc_start: 0.8481 (pp30) cc_final: 0.8074 (pp30) REVERT: C 56 GLU cc_start: 0.7767 (mp0) cc_final: 0.7270 (mp0) REVERT: C 116 GLN cc_start: 0.8905 (tt0) cc_final: 0.8357 (tt0) REVERT: C 120 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7968 (mm-30) REVERT: C 133 PHE cc_start: 0.8865 (m-80) cc_final: 0.8447 (m-80) REVERT: C 203 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.6981 (p90) REVERT: C 237 LEU cc_start: 0.9118 (tp) cc_final: 0.8835 (tt) REVERT: C 401 MET cc_start: 0.8115 (mmm) cc_final: 0.7756 (mmt) REVERT: C 608 ASP cc_start: 0.7505 (p0) cc_final: 0.7011 (p0) REVERT: C 650 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7243 (m-10) REVERT: C 666 PHE cc_start: 0.8368 (t80) cc_final: 0.7617 (t80) REVERT: C 689 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9336 (tm) REVERT: C 843 VAL cc_start: 0.9094 (m) cc_final: 0.8889 (t) REVERT: F 130 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7837 (tm-30) REVERT: F 641 MET cc_start: 0.8496 (mmt) cc_final: 0.7938 (mmt) REVERT: F 656 SER cc_start: 0.8567 (m) cc_final: 0.8352 (p) REVERT: F 687 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7333 (mtp85) REVERT: F 691 LEU cc_start: 0.8661 (mt) cc_final: 0.7878 (pp) REVERT: F 714 MET cc_start: 0.8474 (ttm) cc_final: 0.8260 (ttm) REVERT: F 722 ASP cc_start: 0.7872 (m-30) cc_final: 0.7479 (p0) REVERT: F 830 GLU cc_start: 0.7412 (mp0) cc_final: 0.7047 (mp0) REVERT: G 40 TYR cc_start: 0.8582 (m-80) cc_final: 0.8324 (m-80) REVERT: G 67 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7970 (tp30) REVERT: G 130 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7413 (tm-30) REVERT: G 237 LEU cc_start: 0.9423 (mt) cc_final: 0.9218 (tt) REVERT: G 266 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8395 (mtp) REVERT: G 278 ASP cc_start: 0.8380 (p0) cc_final: 0.8172 (p0) REVERT: G 405 GLN cc_start: 0.7900 (tt0) cc_final: 0.7165 (tp40) REVERT: G 409 ASP cc_start: 0.8334 (m-30) cc_final: 0.8042 (m-30) REVERT: G 443 GLU cc_start: 0.8735 (pp20) cc_final: 0.8222 (pp20) REVERT: G 511 ASN cc_start: 0.8220 (t0) cc_final: 0.7977 (t0) REVERT: G 546 LYS cc_start: 0.8134 (tptp) cc_final: 0.7733 (mmtt) REVERT: G 625 GLN cc_start: 0.7254 (tp40) cc_final: 0.6823 (tm-30) REVERT: G 763 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8798 (pp) REVERT: G 779 MET cc_start: 0.7430 (mmm) cc_final: 0.6503 (pmm) REVERT: L 33 ASP cc_start: 0.8393 (p0) cc_final: 0.8151 (p0) REVERT: L 133 PHE cc_start: 0.8644 (m-80) cc_final: 0.8357 (m-80) REVERT: L 203 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7574 (p90) REVERT: L 251 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7946 (mtm-85) REVERT: L 401 MET cc_start: 0.7901 (mmp) cc_final: 0.7276 (mmt) REVERT: L 434 GLN cc_start: 0.8419 (tp-100) cc_final: 0.8162 (tp-100) REVERT: L 567 SER cc_start: 0.8681 (p) cc_final: 0.8452 (p) REVERT: L 634 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7996 (pptt) REVERT: L 650 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.6194 (t80) REVERT: O 71 GLU cc_start: 0.8660 (tp30) cc_final: 0.8318 (tp30) REVERT: O 120 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8151 (mt-10) REVERT: O 273 ASN cc_start: 0.8589 (t0) cc_final: 0.8263 (t0) REVERT: O 279 LYS cc_start: 0.8888 (mttt) cc_final: 0.8590 (ttmm) REVERT: O 417 SER cc_start: 0.9042 (m) cc_final: 0.8711 (p) REVERT: O 427 GLU cc_start: 0.7907 (tp30) cc_final: 0.7283 (tp30) REVERT: O 428 ASP cc_start: 0.7782 (m-30) cc_final: 0.7121 (m-30) REVERT: O 521 PHE cc_start: 0.6444 (m-80) cc_final: 0.6039 (m-80) outliers start: 113 outliers final: 82 residues processed: 570 average time/residue: 0.2071 time to fit residues: 195.6230 Evaluate side-chains 527 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 433 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 650 PHE Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 689 LEU Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain G residue 804 LEU Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 514 HIS Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 615 LEU Chi-restraints excluded: chain L residue 634 LYS Chi-restraints excluded: chain L residue 650 PHE Chi-restraints excluded: chain L residue 689 LEU Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 763 LEU Chi-restraints excluded: chain L residue 794 GLU Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 570 ILE Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 650 PHE Chi-restraints excluded: chain O residue 654 ILE Chi-restraints excluded: chain O residue 699 ILE Chi-restraints excluded: chain O residue 713 LEU Chi-restraints excluded: chain O residue 722 ASP Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 804 LEU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 338 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 282 optimal weight: 0.0060 chunk 124 optimal weight: 2.9990 chunk 202 optimal weight: 0.2980 chunk 250 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 362 optimal weight: 7.9990 chunk 223 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 overall best weight: 1.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.097029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.074450 restraints weight = 90726.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.076959 restraints weight = 52246.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.078602 restraints weight = 36782.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.079684 restraints weight = 29327.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.080401 restraints weight = 25240.716| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 36685 Z= 0.196 Angle : 0.737 14.294 49588 Z= 0.372 Chirality : 0.048 0.182 5563 Planarity : 0.005 0.096 6283 Dihedral : 6.552 63.896 4891 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.41 % Favored : 89.45 % Rotamer: Outliers : 2.84 % Allowed : 18.34 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.13), residues: 4428 helix: -0.03 (0.13), residues: 1763 sheet: -1.25 (0.23), residues: 510 loop : -2.14 (0.14), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 50 TYR 0.020 0.002 TYR F 721 PHE 0.027 0.001 PHE G 203 TRP 0.045 0.002 TRP L 757 HIS 0.006 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (36683) covalent geometry : angle 0.73710 / 0.37 (49582) hydrogen bonds : bond 0.03968 / 2.59 ( 1239) hydrogen bonds : angle 4.54004 / 3.16 ( 3525) link_TRANS : bond 0.00215 / 0.11 ( 2) link_TRANS : angle 0.53095 / 0.28 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 429 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.6640 (mmp) cc_final: 0.6349 (tpp) REVERT: B 304 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7546 (tt) REVERT: B 342 GLN cc_start: 0.8522 (pp30) cc_final: 0.8144 (pp30) REVERT: C 40 TYR cc_start: 0.8671 (m-80) cc_final: 0.8433 (m-80) REVERT: C 133 PHE cc_start: 0.8974 (m-80) cc_final: 0.8576 (m-80) REVERT: C 401 MET cc_start: 0.8069 (mmm) cc_final: 0.7753 (mmt) REVERT: C 650 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7474 (m-10) REVERT: C 689 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9327 (tm) REVERT: C 722 ASP cc_start: 0.7454 (t0) cc_final: 0.6962 (t0) REVERT: F 130 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7825 (tm-30) REVERT: F 273 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8121 (m110) REVERT: F 687 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7502 (mtp85) REVERT: F 722 ASP cc_start: 0.7907 (m-30) cc_final: 0.7493 (p0) REVERT: G 40 TYR cc_start: 0.8743 (m-80) cc_final: 0.8490 (m-80) REVERT: G 67 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8240 (tp30) REVERT: G 130 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7500 (tm-30) REVERT: G 237 LEU cc_start: 0.9428 (mt) cc_final: 0.9218 (tt) REVERT: G 266 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8497 (mtp) REVERT: G 405 GLN cc_start: 0.8111 (tt0) cc_final: 0.7690 (tp40) REVERT: G 443 GLU cc_start: 0.8782 (pp20) cc_final: 0.8232 (pp20) REVERT: G 497 ASP cc_start: 0.7988 (t70) cc_final: 0.7670 (t0) REVERT: G 511 ASN cc_start: 0.8224 (t0) cc_final: 0.7942 (t0) REVERT: G 546 LYS cc_start: 0.8067 (tptp) cc_final: 0.7803 (mmtt) REVERT: G 557 ASP cc_start: 0.7690 (m-30) cc_final: 0.7474 (m-30) REVERT: G 625 GLN cc_start: 0.7158 (tp40) cc_final: 0.6809 (tm-30) REVERT: G 763 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8830 (pp) REVERT: G 779 MET cc_start: 0.7315 (mmm) cc_final: 0.6637 (pmm) REVERT: L 28 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7502 (ptp-170) REVERT: L 33 ASP cc_start: 0.8433 (p0) cc_final: 0.8183 (p0) REVERT: L 39 LYS cc_start: 0.9489 (OUTLIER) cc_final: 0.9285 (tttm) REVERT: L 203 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7815 (p90) REVERT: L 401 MET cc_start: 0.8018 (mmp) cc_final: 0.7407 (mmt) REVERT: L 434 GLN cc_start: 0.8449 (tp-100) cc_final: 0.8137 (tp-100) REVERT: L 567 SER cc_start: 0.8739 (p) cc_final: 0.8535 (p) REVERT: L 634 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7950 (pmtt) REVERT: L 650 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.6291 (t80) REVERT: L 779 MET cc_start: 0.7830 (mmm) cc_final: 0.7163 (mmm) REVERT: O 71 GLU cc_start: 0.8649 (tp30) cc_final: 0.8311 (tp30) REVERT: O 120 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8207 (mt-10) REVERT: O 273 ASN cc_start: 0.8626 (t0) cc_final: 0.8291 (t0) REVERT: O 279 LYS cc_start: 0.8906 (mttt) cc_final: 0.8608 (ttmm) REVERT: O 417 SER cc_start: 0.9138 (m) cc_final: 0.8811 (p) REVERT: O 427 GLU cc_start: 0.7900 (tp30) cc_final: 0.7256 (tp30) REVERT: O 428 ASP cc_start: 0.7720 (m-30) cc_final: 0.7115 (m-30) REVERT: O 521 PHE cc_start: 0.6412 (m-80) cc_final: 0.5997 (m-80) outliers start: 115 outliers final: 89 residues processed: 518 average time/residue: 0.2088 time to fit residues: 179.2989 Evaluate side-chains 517 residues out of total 4046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 416 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 203 PHE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 514 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 578 ILE Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 650 PHE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 203 PHE Chi-restraints excluded: chain F residue 213 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 514 HIS Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 614 ILE Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 687 ARG Chi-restraints excluded: chain F residue 689 LEU Chi-restraints excluded: chain F residue 732 ILE Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 203 PHE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 493 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 694 THR Chi-restraints excluded: chain G residue 703 GLU Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 741 LEU Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 763 LEU Chi-restraints excluded: chain G residue 804 LEU Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 203 PHE Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 514 HIS Chi-restraints excluded: chain L residue 532 LEU Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 615 LEU Chi-restraints excluded: chain L residue 634 LYS Chi-restraints excluded: chain L residue 650 PHE Chi-restraints excluded: chain L residue 689 LEU Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 763 LEU Chi-restraints excluded: chain O residue 203 PHE Chi-restraints excluded: chain O residue 413 SER Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 532 LEU Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 570 ILE Chi-restraints excluded: chain O residue 615 LEU Chi-restraints excluded: chain O residue 650 PHE Chi-restraints excluded: chain O residue 654 ILE Chi-restraints excluded: chain O residue 699 ILE Chi-restraints excluded: chain O residue 713 LEU Chi-restraints excluded: chain O residue 722 ASP Chi-restraints excluded: chain O residue 741 LEU Chi-restraints excluded: chain O residue 794 GLU Chi-restraints excluded: chain O residue 804 LEU Chi-restraints excluded: chain O residue 839 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 215 optimal weight: 5.9990 chunk 413 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 199 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 429 optimal weight: 0.4980 chunk 295 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 392 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 410 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 450 ASN C 611 ASN ** G 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 273 ASN L 506 ASN ** O 627 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 = 0.3416 r_free = 0.3416 target = 0.100497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.077924 restraints weight = 88282.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.080454 restraints weight = 50220.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.082130 restraints weight = 35218.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.083192 restraints weight = 27996.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.083903 restraints weight = 24111.899| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36685 Z= 0.136 Angle : 0.706 15.619 49588 Z= 0.353 Chirality : 0.047 0.191 5563 Planarity : 0.005 0.096 6283 Dihedral : 6.352 61.605 4891 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.12 % Favored : 90.79 % Rotamer: Outliers : 2.62 % Allowed : 18.59 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.19 % 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: -1.67 (0.13), residues: 4428 helix: 0.03 (0.13), residues: 1769 sheet: -1.27 (0.22), residues: 535 loop : -2.07 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 604 TYR 0.021 0.001 TYR A 143 PHE 0.022 0.001 PHE G 203 TRP 0.046 0.001 TRP L 757 HIS 0.006 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (36683) covalent geometry : angle 0.70618 / 0.35 (49582) hydrogen bonds : bond 0.03462 / 2.28 ( 1239) hydrogen bonds : angle 4.44633 / 3.09 ( 3525) link_TRANS : bond 0.00134 / 0.07 ( 2) link_TRANS : angle 0.51348 / 0.28 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6482.05 seconds wall clock time: 113 minutes 14.29 seconds (6794.29 seconds total)