Starting phenix.real_space_refine on Thu Oct 29 17:17:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygc_72920/10_2026/9ygc_72920.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygc_72920/10_2026/9ygc_72920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ygc_72920/10_2026/9ygc_72920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygc_72920/10_2026/9ygc_72920.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ygc_72920/10_2026/9ygc_72920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygc_72920/10_2026/9ygc_72920.map" } resolution = 3.0 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= 0.006 sd= 0.034 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 Fe 12 7.16 5 S 78 5.16 5 C 20568 2.51 5 N 5910 2.21 5 O 6303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32871 Number of models: 1 Model: "" Number of chains: 24 Chain: "I" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "A" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1766 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 217} Chain: "F" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 311 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "G" Number of atoms: 4642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4642 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 29, 'TRANS': 563} Chain: "B" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "H" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "R" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "T" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1766 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 217} Chain: "L" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 311 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "N" Number of atoms: 4642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4642 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 29, 'TRANS': 563} Chain: "E" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "P" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "S" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "U" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1766 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 217} Chain: "M" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 311 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "O" Number of atoms: 4642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4642 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 29, 'TRANS': 563} Chain: "K" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "Q" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3154 SG CYS J 178 55.984 110.306 131.523 1.00 64.95 S ATOM 3324 SG CYS J 201 62.320 110.045 131.425 1.00 63.86 S ATOM 3042 SG CYS J 165 58.645 104.957 132.387 1.00 35.95 S ATOM 3370 SG CYS J 208 59.218 109.185 137.233 1.00 64.16 S ATOM 14103 SG CYS T 178 32.388 30.860 131.534 1.00 68.91 S ATOM 14273 SG CYS T 201 29.450 36.500 131.483 1.00 69.14 S ATOM 13991 SG CYS T 165 35.676 35.850 132.400 1.00 37.23 S ATOM 14319 SG CYS T 208 31.739 34.222 137.255 1.00 64.22 S ATOM 25052 SG CYS U 178 112.976 50.211 131.535 1.00 65.19 S ATOM 25222 SG CYS U 201 109.590 44.855 131.447 1.00 66.00 S ATOM 24940 SG CYS U 165 107.010 50.586 132.409 1.00 35.46 S ATOM 25268 SG CYS U 208 110.395 47.973 137.251 1.00 63.13 S Time building chain proxies: 7.01, per 1000 atoms: 0.21 Number of scatterers: 32871 At special positions: 0 Unit cell: (132, 134.2, 198, 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) Fe 12 26.01 S 78 16.00 O 6303 8.00 N 5910 7.00 C 20568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 J 301 " pdb="FE1 SF4 J 301 " - pdb=" SG CYS J 178 " pdb="FE4 SF4 J 301 " - pdb=" SG CYS J 208 " pdb="FE3 SF4 J 301 " - pdb=" SG CYS J 165 " pdb="FE2 SF4 J 301 " - pdb=" SG CYS J 201 " pdb=" SF4 T 301 " pdb="FE1 SF4 T 301 " - pdb=" SG CYS T 178 " pdb="FE4 SF4 T 301 " - pdb=" SG CYS T 208 " pdb="FE3 SF4 T 301 " - pdb=" SG CYS T 165 " pdb="FE2 SF4 T 301 " - pdb=" SG CYS T 201 " pdb=" SF4 U 301 " pdb="FE1 SF4 U 301 " - pdb=" SG CYS U 178 " pdb="FE3 SF4 U 301 " - pdb=" SG CYS U 165 " pdb="FE4 SF4 U 301 " - pdb=" SG CYS U 208 " pdb="FE2 SF4 U 301 " - pdb=" SG CYS U 201 " Number of angles added : 36 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7644 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 67 sheets defined 14.4% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'I' and resid 55 through 68 Proline residue: I 60 - end of helix removed outlier: 3.531A pdb=" N HIS I 68 " --> pdb=" O PHE I 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 Proline residue: A 60 - end of helix removed outlier: 3.512A pdb=" N HIS A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 7 Processing helix chain 'J' and resid 24 through 27 Processing helix chain 'J' and resid 79 through 88 removed outlier: 3.818A pdb=" N LEU J 84 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 92 removed outlier: 4.030A pdb=" N VAL J 92 " --> pdb=" O ASP J 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 89 through 92' Processing helix chain 'J' and resid 104 through 106 No H-bonds generated for 'chain 'J' and resid 104 through 106' Processing helix chain 'J' and resid 107 through 111 Processing helix chain 'J' and resid 165 through 170 Processing helix chain 'J' and resid 204 through 213 Processing helix chain 'G' and resid 279 through 289 removed outlier: 3.565A pdb=" N ASP G 285 " --> pdb=" O TRP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 303 Processing helix chain 'G' and resid 304 through 317 removed outlier: 3.611A pdb=" N LEU G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN G 317 " --> pdb=" O GLN G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 351 Processing helix chain 'G' and resid 379 through 383 removed outlier: 3.619A pdb=" N THR G 383 " --> pdb=" O PRO G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 402 removed outlier: 3.816A pdb=" N ARG G 402 " --> pdb=" O GLN G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 416 Processing helix chain 'G' and resid 426 through 434 removed outlier: 3.940A pdb=" N ARG G 432 " --> pdb=" O ARG G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 447 through 465 Processing helix chain 'G' and resid 474 through 480 removed outlier: 3.631A pdb=" N GLY G 479 " --> pdb=" O ASP G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 495 Processing helix chain 'G' and resid 595 through 602 removed outlier: 3.668A pdb=" N LYS G 598 " --> pdb=" O ASN G 595 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE G 599 " --> pdb=" O ALA G 596 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 600 " --> pdb=" O SER G 597 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE G 602 " --> pdb=" O PHE G 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 removed outlier: 3.730A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 88 removed outlier: 3.699A pdb=" N VAL H 80 " --> pdb=" O LEU H 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 68 Proline residue: R 60 - end of helix removed outlier: 3.528A pdb=" N HIS R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 Proline residue: C 60 - end of helix removed outlier: 3.514A pdb=" N HIS C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 7 Processing helix chain 'T' and resid 24 through 27 Processing helix chain 'T' and resid 79 through 88 removed outlier: 3.804A pdb=" N LEU T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 89 through 92 removed outlier: 3.957A pdb=" N VAL T 92 " --> pdb=" O ASP T 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 89 through 92' Processing helix chain 'T' and resid 104 through 106 No H-bonds generated for 'chain 'T' and resid 104 through 106' Processing helix chain 'T' and resid 107 through 111 Processing helix chain 'T' and resid 165 through 170 Processing helix chain 'T' and resid 204 through 213 Processing helix chain 'N' and resid 279 through 289 removed outlier: 3.557A pdb=" N ASP N 285 " --> pdb=" O TRP N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 303 Processing helix chain 'N' and resid 304 through 317 removed outlier: 3.624A pdb=" N LEU N 308 " --> pdb=" O ASP N 304 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN N 317 " --> pdb=" O GLN N 313 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 351 Processing helix chain 'N' and resid 379 through 383 removed outlier: 3.614A pdb=" N THR N 383 " --> pdb=" O PRO N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 398 through 402 Processing helix chain 'N' and resid 413 through 416 Processing helix chain 'N' and resid 426 through 434 removed outlier: 3.954A pdb=" N ARG N 432 " --> pdb=" O ARG N 428 " (cutoff:3.500A) Processing helix chain 'N' and resid 447 through 465 removed outlier: 3.662A pdb=" N GLU N 462 " --> pdb=" O ALA N 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU N 463 " --> pdb=" O LEU N 459 " (cutoff:3.500A) Processing helix chain 'N' and resid 474 through 480 removed outlier: 3.626A pdb=" N GLY N 479 " --> pdb=" O ASP N 476 " (cutoff:3.500A) Processing helix chain 'N' and resid 490 through 495 Processing helix chain 'N' and resid 595 through 602 removed outlier: 3.665A pdb=" N LYS N 598 " --> pdb=" O ASN N 595 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE N 599 " --> pdb=" O ALA N 596 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP N 600 " --> pdb=" O SER N 597 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE N 602 " --> pdb=" O PHE N 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 86 removed outlier: 3.735A pdb=" N SER E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 88 removed outlier: 3.742A pdb=" N VAL P 80 " --> pdb=" O LEU P 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 68 Proline residue: S 60 - end of helix removed outlier: 3.525A pdb=" N HIS S 68 " --> pdb=" O PHE S 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 Proline residue: D 60 - end of helix removed outlier: 3.515A pdb=" N HIS D 68 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 7 Processing helix chain 'U' and resid 24 through 27 Processing helix chain 'U' and resid 79 through 88 removed outlier: 3.804A pdb=" N LEU U 84 " --> pdb=" O SER U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 89 through 92 removed outlier: 3.794A pdb=" N VAL U 92 " --> pdb=" O ASP U 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 89 through 92' Processing helix chain 'U' and resid 104 through 106 No H-bonds generated for 'chain 'U' and resid 104 through 106' Processing helix chain 'U' and resid 107 through 111 Processing helix chain 'U' and resid 165 through 170 Processing helix chain 'U' and resid 204 through 213 Processing helix chain 'O' and resid 279 through 289 removed outlier: 3.554A pdb=" N ASP O 285 " --> pdb=" O TRP O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 303 Processing helix chain 'O' and resid 304 through 317 removed outlier: 3.607A pdb=" N LEU O 308 " --> pdb=" O ASP O 304 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN O 317 " --> pdb=" O GLN O 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 351 Processing helix chain 'O' and resid 379 through 383 removed outlier: 3.626A pdb=" N THR O 383 " --> pdb=" O PRO O 380 " (cutoff:3.500A) Processing helix chain 'O' and resid 398 through 402 removed outlier: 3.684A pdb=" N ARG O 402 " --> pdb=" O GLN O 399 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 416 Processing helix chain 'O' and resid 426 through 434 removed outlier: 3.984A pdb=" N ARG O 432 " --> pdb=" O ARG O 428 " (cutoff:3.500A) Processing helix chain 'O' and resid 447 through 465 removed outlier: 3.686A pdb=" N GLU O 462 " --> pdb=" O ALA O 458 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU O 463 " --> pdb=" O LEU O 459 " (cutoff:3.500A) Processing helix chain 'O' and resid 474 through 480 removed outlier: 3.649A pdb=" N GLY O 479 " --> pdb=" O ASP O 476 " (cutoff:3.500A) Processing helix chain 'O' and resid 490 through 495 Processing helix chain 'O' and resid 595 through 602 removed outlier: 3.689A pdb=" N LYS O 598 " --> pdb=" O ASN O 595 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE O 599 " --> pdb=" O ALA O 596 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP O 600 " --> pdb=" O SER O 597 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE O 602 " --> pdb=" O PHE O 599 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 88 removed outlier: 3.739A pdb=" N SER K 86 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU K 87 " --> pdb=" O PHE K 83 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS K 88 " --> pdb=" O GLN K 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 88 removed outlier: 3.741A pdb=" N VAL Q 80 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 43 through 54 current: chain 'I' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 83 through 87 current: chain 'I' and resid 100 through 110 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 100 through 110 current: chain 'A' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 43 through 54 current: chain 'A' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 87 current: chain 'A' and resid 100 through 109 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 100 through 109 current: chain 'R' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 43 through 54 current: chain 'R' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 83 through 87 current: chain 'R' and resid 100 through 110 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 100 through 110 current: chain 'C' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 43 through 54 current: chain 'C' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 87 current: chain 'C' and resid 100 through 109 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 100 through 109 current: chain 'S' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 43 through 54 current: chain 'S' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 83 through 87 current: chain 'S' and resid 100 through 110 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 100 through 110 current: chain 'D' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 43 through 54 current: chain 'D' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 83 through 87 current: chain 'D' and resid 100 through 109 Processing sheet with id=AA2, first strand: chain 'I' and resid 23 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 27 removed outlier: 7.972A pdb=" N LEU J 15 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY A 37 " --> pdb=" O LEU J 15 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N ARG J 17 " --> pdb=" O GLY A 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 30 through 34 current: chain 'J' and resid 47 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 47 through 51 current: chain 'J' and resid 71 through 75 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 71 through 75 current: chain 'J' and resid 124 through 136 removed outlier: 6.389A pdb=" N GLU J 144 " --> pdb=" O GLU J 131 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS J 133 " --> pdb=" O THR J 142 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR J 142 " --> pdb=" O LYS J 133 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA J 135 " --> pdb=" O GLN J 140 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLN J 140 " --> pdb=" O ALA J 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 60 through 62 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 60 through 62 current: chain 'G' and resid 467 through 473 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 467 through 473 current: chain 'G' and resid 572 through 583 removed outlier: 6.910A pdb=" N THR G 590 " --> pdb=" O MET G 577 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE G 579 " --> pdb=" O GLU G 588 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU G 588 " --> pdb=" O ILE G 579 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ARG G 581 " --> pdb=" O LEU G 586 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU G 586 " --> pdb=" O ARG G 581 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 155 through 156 Processing sheet with id=AA6, first strand: chain 'F' and resid 178 through 180 Processing sheet with id=AA7, first strand: chain 'F' and resid 182 through 185 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 182 through 185 current: chain 'G' and resid 56 through 57 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 188 through 198 removed outlier: 6.746A pdb=" N LEU G 34 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA F 192 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS G 32 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE F 194 " --> pdb=" O ARG G 30 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG G 30 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA F 196 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE G 28 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA G 224 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 89 through 99 removed outlier: 6.578A pdb=" N GLU G 208 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL G 98 " --> pdb=" O ARG G 206 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG G 206 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL G 207 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER G 123 " --> pdb=" O VAL G 207 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA G 209 " --> pdb=" O ARG G 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 106 through 110 removed outlier: 6.507A pdb=" N ILE G 147 " --> pdb=" O GLU G 156 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU G 156 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL G 149 " --> pdb=" O TRP G 154 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TRP G 154 " --> pdb=" O VAL G 149 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AB3, first strand: chain 'G' and resid 250 through 253 Processing sheet with id=AB4, first strand: chain 'G' and resid 256 through 257 removed outlier: 3.536A pdb=" N SER G 262 " --> pdb=" O ASP G 257 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 318 through 320 Processing sheet with id=AB6, first strand: chain 'G' and resid 355 through 359 Processing sheet with id=AB7, first strand: chain 'G' and resid 419 through 425 Processing sheet with id=AB8, first strand: chain 'G' and resid 499 through 506 removed outlier: 6.793A pdb=" N THR G 511 " --> pdb=" O SER G 503 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL G 505 " --> pdb=" O ALA G 509 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA G 509 " --> pdb=" O VAL G 505 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL G 545 " --> pdb=" O VAL G 541 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL G 541 " --> pdb=" O VAL G 545 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER G 547 " --> pdb=" O GLN G 539 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLN G 561 " --> pdb=" O ASN G 527 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 9 through 14 removed outlier: 4.488A pdb=" N ILE B 10 " --> pdb=" O ILE B 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 24 through 28 current: chain 'B' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 65 through 71 current: chain 'B' and resid 125 through 134 removed outlier: 6.779A pdb=" N THR B 150 " --> pdb=" O SER B 133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 41 through 45 removed outlier: 4.494A pdb=" N ASP B 42 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AC3, first strand: chain 'B' and resid 137 through 139 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 137 through 139 current: chain 'Q' and resid 24 through 28 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 24 through 28 current: chain 'Q' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 65 through 71 current: chain 'Q' and resid 125 through 134 removed outlier: 7.106A pdb=" N THR Q 150 " --> pdb=" O SER Q 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 9 through 14 removed outlier: 4.242A pdb=" N ILE H 10 " --> pdb=" O ILE H 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 24 through 28 current: chain 'H' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 65 through 71 current: chain 'H' and resid 125 through 134 removed outlier: 7.130A pdb=" N THR H 150 " --> pdb=" O SER H 133 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 41 through 45 removed outlier: 4.435A pdb=" N ASP H 42 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 109 through 110 Processing sheet with id=AC7, first strand: chain 'R' and resid 23 through 27 Processing sheet with id=AC8, first strand: chain 'C' and resid 24 through 27 removed outlier: 7.975A pdb=" N LEU T 15 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY C 37 " --> pdb=" O LEU T 15 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N ARG T 17 " --> pdb=" O GLY C 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 30 through 34 current: chain 'T' and resid 47 through 51 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 47 through 51 current: chain 'T' and resid 71 through 75 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 71 through 75 current: chain 'T' and resid 124 through 136 removed outlier: 6.382A pdb=" N GLU T 144 " --> pdb=" O GLU T 131 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS T 133 " --> pdb=" O THR T 142 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR T 142 " --> pdb=" O LYS T 133 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA T 135 " --> pdb=" O GLN T 140 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN T 140 " --> pdb=" O ALA T 135 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 60 through 62 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 60 through 62 current: chain 'N' and resid 467 through 473 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 467 through 473 current: chain 'N' and resid 572 through 583 removed outlier: 6.903A pdb=" N THR N 590 " --> pdb=" O MET N 577 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE N 579 " --> pdb=" O GLU N 588 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLU N 588 " --> pdb=" O ILE N 579 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG N 581 " --> pdb=" O LEU N 586 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU N 586 " --> pdb=" O ARG N 581 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 155 through 156 Processing sheet with id=AD2, first strand: chain 'L' and resid 178 through 180 Processing sheet with id=AD3, first strand: chain 'L' and resid 182 through 185 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 182 through 185 current: chain 'N' and resid 56 through 57 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'L' and resid 188 through 198 removed outlier: 6.757A pdb=" N LEU N 34 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA L 192 " --> pdb=" O LYS N 32 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS N 32 " --> pdb=" O ALA L 192 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE L 194 " --> pdb=" O ARG N 30 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG N 30 " --> pdb=" O ILE L 194 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA L 196 " --> pdb=" O ILE N 28 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE N 28 " --> pdb=" O ALA L 196 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA N 224 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 89 through 99 removed outlier: 6.638A pdb=" N GLU N 208 " --> pdb=" O VAL N 96 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL N 98 " --> pdb=" O ARG N 206 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG N 206 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL N 207 " --> pdb=" O SER N 123 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER N 123 " --> pdb=" O VAL N 207 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA N 209 " --> pdb=" O ARG N 121 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 106 through 110 removed outlier: 6.499A pdb=" N ILE N 147 " --> pdb=" O GLU N 156 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU N 156 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL N 149 " --> pdb=" O TRP N 154 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TRP N 154 " --> pdb=" O VAL N 149 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 129 through 130 Processing sheet with id=AD8, first strand: chain 'N' and resid 250 through 253 Processing sheet with id=AD9, first strand: chain 'N' and resid 256 through 257 removed outlier: 3.531A pdb=" N SER N 262 " --> pdb=" O ASP N 257 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 318 through 320 Processing sheet with id=AE2, first strand: chain 'N' and resid 355 through 359 Processing sheet with id=AE3, first strand: chain 'N' and resid 419 through 425 Processing sheet with id=AE4, first strand: chain 'N' and resid 499 through 506 removed outlier: 6.782A pdb=" N THR N 511 " --> pdb=" O SER N 503 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL N 505 " --> pdb=" O ALA N 509 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA N 509 " --> pdb=" O VAL N 505 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL N 545 " --> pdb=" O VAL N 541 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL N 541 " --> pdb=" O VAL N 545 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER N 547 " --> pdb=" O GLN N 539 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLN N 561 " --> pdb=" O ASN N 527 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 9 through 14 removed outlier: 4.491A pdb=" N ILE E 10 " --> pdb=" O ILE E 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 24 through 28 current: chain 'E' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 65 through 71 current: chain 'E' and resid 125 through 134 removed outlier: 6.765A pdb=" N THR E 150 " --> pdb=" O SER E 133 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 41 through 45 removed outlier: 4.895A pdb=" N LEU E 60 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE E 44 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS E 58 " --> pdb=" O ILE E 44 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AE8, first strand: chain 'P' and resid 9 through 14 removed outlier: 4.225A pdb=" N ILE P 10 " --> pdb=" O ILE P 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 24 through 28 current: chain 'P' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 65 through 71 current: chain 'P' and resid 125 through 134 removed outlier: 7.108A pdb=" N THR P 150 " --> pdb=" O SER P 133 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 41 through 45 removed outlier: 4.508A pdb=" N ASP P 42 " --> pdb=" O GLY P 59 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 109 through 110 Processing sheet with id=AF2, first strand: chain 'S' and resid 23 through 27 Processing sheet with id=AF3, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.978A pdb=" N LEU U 15 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY D 37 " --> pdb=" O LEU U 15 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ARG U 17 " --> pdb=" O GLY D 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 30 through 34 current: chain 'U' and resid 47 through 51 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 47 through 51 current: chain 'U' and resid 71 through 75 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 71 through 75 current: chain 'U' and resid 124 through 136 removed outlier: 6.414A pdb=" N GLU U 144 " --> pdb=" O GLU U 131 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS U 133 " --> pdb=" O THR U 142 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR U 142 " --> pdb=" O LYS U 133 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA U 135 " --> pdb=" O GLN U 140 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN U 140 " --> pdb=" O ALA U 135 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 60 through 62 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 60 through 62 current: chain 'O' and resid 468 through 473 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 468 through 473 current: chain 'O' and resid 572 through 583 removed outlier: 6.910A pdb=" N THR O 590 " --> pdb=" O MET O 577 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE O 579 " --> pdb=" O GLU O 588 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU O 588 " --> pdb=" O ILE O 579 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARG O 581 " --> pdb=" O LEU O 586 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU O 586 " --> pdb=" O ARG O 581 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 155 through 156 Processing sheet with id=AF6, first strand: chain 'M' and resid 178 through 180 Processing sheet with id=AF7, first strand: chain 'M' and resid 182 through 185 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 182 through 185 current: chain 'O' and resid 56 through 57 No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'M' and resid 188 through 198 removed outlier: 6.747A pdb=" N LEU O 34 " --> pdb=" O ILE M 190 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA M 192 " --> pdb=" O LYS O 32 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS O 32 " --> pdb=" O ALA M 192 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE M 194 " --> pdb=" O ARG O 30 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG O 30 " --> pdb=" O ILE M 194 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA M 196 " --> pdb=" O ILE O 28 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE O 28 " --> pdb=" O ALA M 196 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA O 224 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 89 through 99 removed outlier: 6.587A pdb=" N GLU O 208 " --> pdb=" O VAL O 96 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL O 98 " --> pdb=" O ARG O 206 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG O 206 " --> pdb=" O VAL O 98 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL O 207 " --> pdb=" O SER O 123 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER O 123 " --> pdb=" O VAL O 207 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA O 209 " --> pdb=" O ARG O 121 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 106 through 110 removed outlier: 6.538A pdb=" N ILE O 147 " --> pdb=" O GLU O 156 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU O 156 " --> pdb=" O ILE O 147 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL O 149 " --> pdb=" O TRP O 154 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TRP O 154 " --> pdb=" O VAL O 149 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 129 through 130 Processing sheet with id=AG3, first strand: chain 'O' and resid 250 through 253 Processing sheet with id=AG4, first strand: chain 'O' and resid 256 through 257 removed outlier: 3.533A pdb=" N SER O 262 " --> pdb=" O ASP O 257 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 318 through 320 Processing sheet with id=AG6, first strand: chain 'O' and resid 355 through 359 Processing sheet with id=AG7, first strand: chain 'O' and resid 419 through 425 Processing sheet with id=AG8, first strand: chain 'O' and resid 499 through 506 removed outlier: 6.779A pdb=" N THR O 511 " --> pdb=" O SER O 503 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL O 505 " --> pdb=" O ALA O 509 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA O 509 " --> pdb=" O VAL O 505 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL O 545 " --> pdb=" O VAL O 541 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL O 541 " --> pdb=" O VAL O 545 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER O 547 " --> pdb=" O GLN O 539 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 9 through 14 removed outlier: 4.494A pdb=" N ILE K 10 " --> pdb=" O ILE K 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 24 through 28 current: chain 'K' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 65 through 71 current: chain 'K' and resid 125 through 134 removed outlier: 6.773A pdb=" N THR K 150 " --> pdb=" O SER K 133 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 41 through 45 removed outlier: 4.901A pdb=" N LEU K 60 " --> pdb=" O ASP K 42 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE K 44 " --> pdb=" O LYS K 58 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LYS K 58 " --> pdb=" O ILE K 44 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 109 through 110 Processing sheet with id=AH3, first strand: chain 'Q' and resid 41 through 45 removed outlier: 4.515A pdb=" N ASP Q 42 " --> pdb=" O GLY Q 59 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 109 through 110 698 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.91 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 14116 1.40 - 1.59: 19397 1.59 - 1.77: 0 1.77 - 1.95: 96 1.95 - 2.14: 36 Bond restraints: 33645 Sorted by residual: bond pdb=" S1 SF4 J 301 " pdb="FE2 SF4 J 301 " ideal model delta sigma weight residual 2.280 2.134 0.146 3.00e-02 1.11e+03 2.37e+01 bond pdb=" S3 SF4 J 301 " pdb="FE1 SF4 J 301 " ideal model delta sigma weight residual 2.280 2.134 0.146 3.00e-02 1.11e+03 2.35e+01 bond pdb=" S3 SF4 T 301 " pdb="FE2 SF4 T 301 " ideal model delta sigma weight residual 2.280 2.135 0.145 3.00e-02 1.11e+03 2.35e+01 bond pdb=" S4 SF4 T 301 " pdb="FE1 SF4 T 301 " ideal model delta sigma weight residual 2.280 2.135 0.145 3.00e-02 1.11e+03 2.35e+01 bond pdb=" S2 SF4 T 301 " pdb="FE1 SF4 T 301 " ideal model delta sigma weight residual 2.280 2.135 0.145 3.00e-02 1.11e+03 2.35e+01 ... (remaining 33640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 45565 3.27 - 6.53: 144 6.53 - 9.80: 2 9.80 - 13.07: 0 13.07 - 16.34: 72 Bond angle restraints: 45783 Sorted by residual: angle pdb="FE2 SF4 T 301 " pdb=" S1 SF4 T 301 " pdb="FE3 SF4 T 301 " ideal model delta sigma weight residual 73.70 90.04 -16.34 1.50e+00 4.44e-01 1.19e+02 angle pdb="FE2 SF4 U 301 " pdb=" S4 SF4 U 301 " pdb="FE3 SF4 U 301 " ideal model delta sigma weight residual 73.70 90.03 -16.33 1.50e+00 4.44e-01 1.18e+02 angle pdb="FE1 SF4 U 301 " pdb=" S2 SF4 U 301 " pdb="FE4 SF4 U 301 " ideal model delta sigma weight residual 73.70 90.03 -16.33 1.50e+00 4.44e-01 1.18e+02 angle pdb="FE1 SF4 U 301 " pdb=" S3 SF4 U 301 " pdb="FE4 SF4 U 301 " ideal model delta sigma weight residual 73.70 90.03 -16.33 1.50e+00 4.44e-01 1.18e+02 angle pdb="FE2 SF4 T 301 " pdb=" S4 SF4 T 301 " pdb="FE3 SF4 T 301 " ideal model delta sigma weight residual 73.70 90.02 -16.32 1.50e+00 4.44e-01 1.18e+02 ... (remaining 45778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 18275 17.94 - 35.88: 1142 35.88 - 53.83: 284 53.83 - 71.77: 91 71.77 - 89.71: 32 Dihedral angle restraints: 19824 sinusoidal: 7845 harmonic: 11979 Sorted by residual: dihedral pdb=" CA LEU G 218 " pdb=" C LEU G 218 " pdb=" N ARG G 219 " pdb=" CA ARG G 219 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LEU N 218 " pdb=" C LEU N 218 " pdb=" N ARG N 219 " pdb=" CA ARG N 219 " ideal model delta harmonic sigma weight residual 180.00 152.14 27.86 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA LEU O 218 " pdb=" C LEU O 218 " pdb=" N ARG O 219 " pdb=" CA ARG O 219 " ideal model delta harmonic sigma weight residual 180.00 152.17 27.83 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 19821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 4914 0.166 - 0.331: 0 0.331 - 0.497: 0 0.497 - 0.662: 0 0.662 - 0.828: 12 Chirality restraints: 4926 Sorted by residual: chirality pdb="FE2 SF4 J 301 " pdb=" S1 SF4 J 301 " pdb=" S3 SF4 J 301 " pdb=" S4 SF4 J 301 " both_signs ideal model delta sigma weight residual False 10.55 9.73 0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb="FE1 SF4 T 301 " pdb=" S2 SF4 T 301 " pdb=" S3 SF4 T 301 " pdb=" S4 SF4 T 301 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb="FE2 SF4 U 301 " pdb=" S1 SF4 U 301 " pdb=" S3 SF4 U 301 " pdb=" S4 SF4 U 301 " both_signs ideal model delta sigma weight residual False 10.55 9.73 0.83 2.00e-01 2.50e+01 1.70e+01 ... (remaining 4923 not shown) Planarity restraints: 6102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 135 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.22e+00 pdb=" N PRO H 136 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 136 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 136 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE P 135 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO P 136 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO P 136 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO P 136 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE Q 135 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO Q 136 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO Q 136 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO Q 136 " 0.024 5.00e-02 4.00e+02 ... (remaining 6099 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 507 2.69 - 3.24: 30643 3.24 - 3.79: 46616 3.79 - 4.35: 67924 4.35 - 4.90: 114882 Nonbonded interactions: 260572 Sorted by model distance: nonbonded pdb=" O GLN J 117 " pdb=" OE1 GLN J 117 " model vdw 2.135 3.040 nonbonded pdb=" OE1 GLN S 48 " pdb=" OG1 THR S 106 " model vdw 2.205 3.040 nonbonded pdb=" OE1 GLN I 48 " pdb=" OG1 THR I 106 " model vdw 2.212 3.040 nonbonded pdb=" O ASP U 89 " pdb=" OD1 ASP U 89 " model vdw 2.246 3.040 nonbonded pdb=" NH1 ARG N 398 " pdb=" OE1 GLN U 132 " model vdw 2.258 3.120 ... (remaining 260567 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'I' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'J' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 34.220 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 0.172 33657 Z= 0.241 Angle : 0.939 20.591 45819 Z= 0.536 Chirality : 0.060 0.828 4926 Planarity : 0.005 0.046 6102 Dihedral : 13.739 89.710 12180 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.32 % Allowed : 6.52 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.12), residues: 4200 helix: -0.63 (0.25), residues: 414 sheet: 0.66 (0.13), residues: 1506 loop : -0.18 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 398 TYR 0.018 0.002 TYR A 28 PHE 0.017 0.001 PHE G 235 TRP 0.023 0.002 TRP G 457 HIS 0.008 0.002 HIS N 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.22 (33645) covalent geometry : angle 0.87348 / 0.53 (45783) hydrogen bonds : bond 0.19356 / 12.74 ( 698) hydrogen bonds : angle 7.62229 / 5.24 ( 1818) metal coordination : bond 0.17015 / 10.40 ( 12) metal coordination : angle 12.33516 / 7.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 258 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 GLN cc_start: 0.8006 (tt0) cc_final: 0.7779 (tm-30) REVERT: E 65 GLN cc_start: 0.8023 (tt0) cc_final: 0.7670 (tm-30) REVERT: K 39 ASN cc_start: 0.8333 (t0) cc_final: 0.8087 (t0) REVERT: K 65 GLN cc_start: 0.8078 (tt0) cc_final: 0.7651 (tm-30) REVERT: K 131 TYR cc_start: 0.7023 (p90) cc_final: 0.6813 (p90) outliers start: 11 outliers final: 4 residues processed: 265 average time/residue: 0.8385 time to fit residues: 257.5764 Evaluate side-chains 135 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain S residue 12 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 401, 155, 244] chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 108 GLN A 104 ASN J 126 ASN G 111 ASN G 333 ASN G 456 GLN G 561 GLN ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 594 HIS B 39 ASN B 43 GLN ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 ASN N 561 GLN N 594 HIS E 39 ASN U 126 ASN O 333 ASN O 561 GLN O 594 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.078667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.056812 restraints weight = 109286.299| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.43 r_work: 0.3170 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 33657 Z= 0.363 Angle : 0.740 13.428 45819 Z= 0.380 Chirality : 0.049 0.168 4926 Planarity : 0.006 0.061 6102 Dihedral : 5.492 30.736 4652 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.46 % Allowed : 8.32 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.12), residues: 4200 helix: -0.32 (0.26), residues: 426 sheet: 0.33 (0.13), residues: 1521 loop : -0.55 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 81 TYR 0.023 0.003 TYR E 131 PHE 0.019 0.002 PHE P 126 TRP 0.026 0.002 TRP J 143 HIS 0.011 0.002 HIS N 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00857 / 0.36 (33645) covalent geometry : angle 0.71787 / 0.38 (45783) hydrogen bonds : bond 0.05078 / 3.38 ( 698) hydrogen bonds : angle 5.91431 / 4.06 ( 1818) metal coordination : bond 0.02851 / 1.70 ( 12) metal coordination : angle 6.41958 / 3.92 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 131 time to evaluate : 1.348 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: I 45 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8754 (mm-30) REVERT: I 82 GLU cc_start: 0.8203 (mp0) cc_final: 0.7856 (mp0) REVERT: A 45 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8528 (mt-10) REVERT: J 185 MET cc_start: 0.8517 (mtm) cc_final: 0.8209 (mmm) REVERT: G 182 ARG cc_start: 0.8990 (mtp-110) cc_final: 0.8581 (ttm110) REVERT: B 113 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8040 (tm-30) REVERT: R 5 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7807 (mt-10) REVERT: R 10 ASP cc_start: 0.8578 (p0) cc_final: 0.8074 (p0) REVERT: R 63 ASP cc_start: 0.9088 (t0) cc_final: 0.8843 (t0) REVERT: R 82 GLU cc_start: 0.8099 (mp0) cc_final: 0.7889 (mp0) REVERT: T 117 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7820 (tp40) REVERT: T 185 MET cc_start: 0.8869 (mtp) cc_final: 0.8399 (mmm) REVERT: N 506 ASP cc_start: 0.8504 (t0) cc_final: 0.8251 (t0) REVERT: E 113 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8164 (tm-30) REVERT: E 129 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6939 (tm-30) REVERT: P 61 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8100 (mtp180) REVERT: U 195 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8756 (t0) REVERT: K 95 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7607 (ptmm) REVERT: K 113 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8028 (tm-30) REVERT: K 134 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7066 (m-30) outliers start: 85 outliers final: 16 residues processed: 199 average time/residue: 0.7537 time to fit residues: 177.5396 Evaluate side-chains 138 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 215 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 311 ILE Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain U residue 195 ASP Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 205 MET Chi-restraints excluded: chain O residue 506 ASP Chi-restraints excluded: chain K residue 95 LYS Chi-restraints excluded: chain K residue 134 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [264, 60, 323, 61, 354, 393, 243, 122, 281, 24, 154] chunk 264 optimal weight: 30.0000 chunk 60 optimal weight: 9.9990 chunk 323 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 354 optimal weight: 0.7980 chunk 393 optimal weight: 9.9990 chunk 243 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 281 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 108 GLN ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS N 333 ASN N 561 GLN O 561 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.080662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.058507 restraints weight = 109364.202| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.54 r_work: 0.3227 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33657 Z= 0.138 Angle : 0.544 11.134 45819 Z= 0.275 Chirality : 0.042 0.140 4926 Planarity : 0.004 0.063 6102 Dihedral : 4.735 24.639 4649 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.54 % Allowed : 9.13 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4200 helix: 0.12 (0.26), residues: 429 sheet: 0.48 (0.13), residues: 1473 loop : -0.43 (0.12), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 75 TYR 0.016 0.001 TYR E 131 PHE 0.010 0.001 PHE O 353 TRP 0.016 0.001 TRP J 143 HIS 0.005 0.001 HIS N 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (33645) covalent geometry : angle 0.51952 / 0.27 (45783) hydrogen bonds : bond 0.03533 / 2.37 ( 698) hydrogen bonds : angle 5.25725 / 3.60 ( 1818) metal coordination : bond 0.00663 / 0.38 ( 12) metal coordination : angle 5.76984 / 3.49 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 131 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 45 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8725 (mm-30) REVERT: I 82 GLU cc_start: 0.8261 (mp0) cc_final: 0.7844 (mp0) REVERT: J 117 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: J 185 MET cc_start: 0.8501 (mtm) cc_final: 0.8286 (mtm) REVERT: B 65 GLN cc_start: 0.8324 (tt0) cc_final: 0.6946 (tm-30) REVERT: B 113 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8058 (tm-30) REVERT: H 137 PHE cc_start: 0.6021 (m-10) cc_final: 0.5722 (m-80) REVERT: R 5 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7849 (mt-10) REVERT: R 10 ASP cc_start: 0.8553 (p0) cc_final: 0.7866 (p0) REVERT: R 63 ASP cc_start: 0.9108 (t0) cc_final: 0.8752 (t0) REVERT: R 82 GLU cc_start: 0.8127 (mp0) cc_final: 0.7837 (mp0) REVERT: C 10 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7702 (t70) REVERT: T 117 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7929 (tp40) REVERT: T 185 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8373 (mmm) REVERT: N 506 ASP cc_start: 0.8434 (t0) cc_final: 0.8112 (t0) REVERT: E 65 GLN cc_start: 0.8327 (tt0) cc_final: 0.8076 (tt0) REVERT: E 113 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8108 (tm-30) REVERT: E 129 GLU cc_start: 0.7290 (tm-30) cc_final: 0.7050 (tm-30) REVERT: P 48 CYS cc_start: 0.8197 (OUTLIER) cc_final: 0.6891 (t) REVERT: P 87 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7352 (mp0) REVERT: P 88 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8649 (mmtm) REVERT: K 113 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8031 (tm-30) REVERT: Q 61 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8056 (ptp-110) REVERT: Q 87 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7531 (mp0) outliers start: 53 outliers final: 17 residues processed: 171 average time/residue: 0.7588 time to fit residues: 152.9605 Evaluate side-chains 138 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 117 GLN Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain U residue 193 VAL Chi-restraints excluded: chain O residue 205 MET Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 506 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain Q residue 61 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [70, 353, 363, 43, 131, 153, 0, 85, 13, 391, 14] chunk 70 optimal weight: 6.9990 chunk 353 optimal weight: 2.9990 chunk 363 optimal weight: 0.0270 chunk 43 optimal weight: 10.0000 chunk 131 optimal weight: 40.0000 chunk 153 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 391 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 overall best weight: 5.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 81 GLN ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN N 561 GLN U 38 GLN O 81 GLN O 83 HIS O 561 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.078799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.056790 restraints weight = 108512.303| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.46 r_work: 0.3191 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 33657 Z= 0.236 Angle : 0.589 11.835 45819 Z= 0.296 Chirality : 0.044 0.143 4926 Planarity : 0.005 0.060 6102 Dihedral : 4.720 24.516 4647 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.97 % Allowed : 9.62 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 4200 helix: 0.34 (0.27), residues: 426 sheet: 0.39 (0.14), residues: 1434 loop : -0.56 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 75 TYR 0.015 0.002 TYR N 284 PHE 0.017 0.002 PHE B 117 TRP 0.015 0.001 TRP J 143 HIS 0.007 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (33645) covalent geometry : angle 0.56314 / 0.30 (45783) hydrogen bonds : bond 0.03849 / 2.59 ( 698) hydrogen bonds : angle 5.21969 / 3.56 ( 1818) metal coordination : bond 0.01577 / 0.94 ( 12) metal coordination : angle 6.14522 / 3.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 121 time to evaluate : 1.288 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: I 45 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8705 (mm-30) REVERT: I 82 GLU cc_start: 0.8346 (mp0) cc_final: 0.7905 (mp0) REVERT: J 117 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: J 185 MET cc_start: 0.8684 (mtm) cc_final: 0.8249 (mtm) REVERT: J 195 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8484 (p0) REVERT: G 81 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7634 (mt0) REVERT: B 65 GLN cc_start: 0.8406 (tt0) cc_final: 0.7129 (tm130) REVERT: B 113 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8104 (tm-30) REVERT: H 162 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7490 (mmtm) REVERT: R 5 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7828 (mt-10) REVERT: R 10 ASP cc_start: 0.8532 (p0) cc_final: 0.7875 (p0) REVERT: R 45 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8596 (mm-30) REVERT: R 63 ASP cc_start: 0.9134 (t0) cc_final: 0.8721 (t0) REVERT: R 82 GLU cc_start: 0.8260 (mp0) cc_final: 0.8059 (mp0) REVERT: C 10 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7694 (t70) REVERT: C 45 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: T 117 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: T 185 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8401 (mmm) REVERT: N 506 ASP cc_start: 0.8531 (t0) cc_final: 0.8172 (t0) REVERT: E 65 GLN cc_start: 0.8357 (tt0) cc_final: 0.8106 (tt0) REVERT: E 95 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7474 (pttp) REVERT: E 113 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8120 (tm-30) REVERT: E 129 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7135 (tm-30) REVERT: P 48 CYS cc_start: 0.8214 (OUTLIER) cc_final: 0.6951 (t) REVERT: P 87 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7375 (mp0) REVERT: S 63 ASP cc_start: 0.9040 (t0) cc_final: 0.8752 (t0) REVERT: O 343 TRP cc_start: 0.8399 (OUTLIER) cc_final: 0.8149 (t60) REVERT: K 113 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8089 (tm-30) REVERT: Q 61 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8106 (ptp-110) outliers start: 68 outliers final: 26 residues processed: 172 average time/residue: 0.7221 time to fit residues: 147.9567 Evaluate side-chains 153 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 117 GLN Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 311 ILE Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain T residue 195 ASP Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 205 MET Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 162 LYS Chi-restraints excluded: chain U residue 191 ASN Chi-restraints excluded: chain U residue 193 VAL Chi-restraints excluded: chain O residue 205 MET Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 343 TRP Chi-restraints excluded: chain O residue 435 ILE Chi-restraints excluded: chain O residue 506 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 95 LYS Chi-restraints excluded: chain Q residue 61 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [359, 382, 9, 170, 190, 151, 178, 280, 12, 396, 55] chunk 359 optimal weight: 6.9990 chunk 382 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 170 optimal weight: 0.0670 chunk 190 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 280 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 396 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 38 GLN G 81 GLN G 83 HIS ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 38 GLN N 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.079271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.057611 restraints weight = 108308.597| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.43 r_work: 0.3206 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33657 Z= 0.172 Angle : 0.542 12.203 45819 Z= 0.269 Chirality : 0.042 0.138 4926 Planarity : 0.004 0.056 6102 Dihedral : 4.513 23.257 4647 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.91 % Allowed : 10.03 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 4200 helix: 0.48 (0.26), residues: 444 sheet: 0.43 (0.14), residues: 1431 loop : -0.57 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 182 TYR 0.016 0.001 TYR B 131 PHE 0.016 0.001 PHE B 117 TRP 0.013 0.001 TRP G 343 HIS 0.005 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (33645) covalent geometry : angle 0.51379 / 0.27 (45783) hydrogen bonds : bond 0.03333 / 2.24 ( 698) hydrogen bonds : angle 4.99233 / 3.41 ( 1818) metal coordination : bond 0.00986 / 0.58 ( 12) metal coordination : angle 6.20725 / 3.89 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 125 time to evaluate : 1.120 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: I 45 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8709 (mm-30) REVERT: I 82 GLU cc_start: 0.8297 (mp0) cc_final: 0.7865 (mp0) REVERT: J 117 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: J 185 MET cc_start: 0.8731 (mtm) cc_final: 0.8223 (mtm) REVERT: B 26 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.5663 (pp) REVERT: B 65 GLN cc_start: 0.8420 (tt0) cc_final: 0.7173 (tm130) REVERT: B 91 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8427 (tp30) REVERT: B 113 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8044 (tm-30) REVERT: R 5 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7868 (mt-10) REVERT: R 10 ASP cc_start: 0.8543 (p0) cc_final: 0.7855 (p0) REVERT: R 45 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8536 (mm-30) REVERT: R 63 ASP cc_start: 0.9130 (t0) cc_final: 0.8725 (t0) REVERT: C 10 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7669 (t70) REVERT: C 45 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: T 117 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: T 185 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8439 (mmm) REVERT: T 195 ASP cc_start: 0.9133 (t0) cc_final: 0.8520 (p0) REVERT: N 400 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8117 (ttm-80) REVERT: N 506 ASP cc_start: 0.8537 (t0) cc_final: 0.8196 (OUTLIER) REVERT: E 65 GLN cc_start: 0.8352 (tt0) cc_final: 0.8100 (tt0) REVERT: E 95 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7249 (pttt) REVERT: E 113 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8130 (tm-30) REVERT: E 129 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7077 (tm-30) REVERT: P 48 CYS cc_start: 0.8215 (OUTLIER) cc_final: 0.6923 (t) REVERT: P 87 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7379 (mp0) REVERT: S 63 ASP cc_start: 0.9050 (t0) cc_final: 0.8741 (t0) REVERT: O 343 TRP cc_start: 0.8412 (OUTLIER) cc_final: 0.8145 (t60) REVERT: K 65 GLN cc_start: 0.8429 (tt0) cc_final: 0.7124 (tm130) REVERT: K 113 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8103 (tm-30) REVERT: Q 61 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8088 (ptp-110) outliers start: 66 outliers final: 27 residues processed: 175 average time/residue: 0.7477 time to fit residues: 155.1978 Evaluate side-chains 153 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 117 GLN Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain T residue 30 MET Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 88 LYS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain U residue 193 VAL Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 205 MET Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 343 TRP Chi-restraints excluded: chain O residue 435 ILE Chi-restraints excluded: chain O residue 506 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 95 LYS Chi-restraints excluded: chain Q residue 61 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [285, 11, 66, 148, 263, 37, 335, 46, 233, 121, 299] chunk 285 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 66 optimal weight: 50.0000 chunk 148 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 335 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 299 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 81 GLN ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.079289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.057451 restraints weight = 107845.413| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.45 r_work: 0.3207 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33657 Z= 0.160 Angle : 0.540 12.007 45819 Z= 0.266 Chirality : 0.042 0.135 4926 Planarity : 0.004 0.055 6102 Dihedral : 4.380 22.616 4647 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.80 % Allowed : 10.46 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 4200 helix: 0.81 (0.27), residues: 426 sheet: 0.43 (0.14), residues: 1431 loop : -0.51 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 182 TYR 0.014 0.001 TYR B 131 PHE 0.012 0.001 PHE B 117 TRP 0.018 0.001 TRP G 343 HIS 0.005 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (33645) covalent geometry : angle 0.51217 / 0.27 (45783) hydrogen bonds : bond 0.03170 / 2.13 ( 698) hydrogen bonds : angle 4.87412 / 3.32 ( 1818) metal coordination : bond 0.00908 / 0.53 ( 12) metal coordination : angle 6.17030 / 3.86 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 121 time to evaluate : 1.040 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: I 45 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8724 (mm-30) REVERT: I 82 GLU cc_start: 0.8316 (mp0) cc_final: 0.7914 (mp0) REVERT: J 117 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: J 185 MET cc_start: 0.8730 (mtm) cc_final: 0.8139 (mtm) REVERT: B 26 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5651 (pp) REVERT: B 65 GLN cc_start: 0.8417 (tt0) cc_final: 0.7137 (tm130) REVERT: B 113 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8092 (tm-30) REVERT: H 162 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7996 (mmtm) REVERT: R 5 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7874 (mt-10) REVERT: R 10 ASP cc_start: 0.8536 (p0) cc_final: 0.7864 (p0) REVERT: R 45 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8574 (mm-30) REVERT: R 63 ASP cc_start: 0.9123 (t0) cc_final: 0.8726 (t0) REVERT: R 82 GLU cc_start: 0.8268 (mp0) cc_final: 0.7998 (mp0) REVERT: C 10 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7624 (t70) REVERT: C 45 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8468 (mt-10) REVERT: T 117 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: T 185 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8417 (mmm) REVERT: N 400 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8113 (ttm-80) REVERT: N 506 ASP cc_start: 0.8577 (t0) cc_final: 0.8255 (OUTLIER) REVERT: N 577 MET cc_start: 0.8411 (mmp) cc_final: 0.8058 (mmp) REVERT: E 4 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6614 (tm) REVERT: E 65 GLN cc_start: 0.8360 (tt0) cc_final: 0.8109 (tt0) REVERT: E 113 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8150 (tm-30) REVERT: E 129 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7139 (tm-30) REVERT: P 48 CYS cc_start: 0.8243 (OUTLIER) cc_final: 0.6984 (t) REVERT: P 87 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7130 (mp0) REVERT: P 88 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8608 (mmtm) REVERT: O 343 TRP cc_start: 0.8423 (OUTLIER) cc_final: 0.8123 (t60) REVERT: K 65 GLN cc_start: 0.8414 (tt0) cc_final: 0.7085 (tm-30) REVERT: K 91 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8451 (tp30) REVERT: K 113 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8201 (tm-30) REVERT: Q 61 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8099 (ptp-110) REVERT: Q 137 PHE cc_start: 0.6033 (OUTLIER) cc_final: 0.5397 (m-80) outliers start: 62 outliers final: 26 residues processed: 169 average time/residue: 0.6822 time to fit residues: 137.4927 Evaluate side-chains 155 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 117 GLN Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain T residue 30 MET Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 88 LYS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain U residue 193 VAL Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 205 MET Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 343 TRP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 95 LYS Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 137 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [192, 227, 5, 143, 349, 193, 237, 249, 208, 226, 326] chunk 192 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 349 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 237 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 208 optimal weight: 0.7980 chunk 226 optimal weight: 0.9990 chunk 326 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 ASN ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.079481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.057535 restraints weight = 110153.894| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.52 r_work: 0.3208 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33657 Z= 0.152 Angle : 0.540 11.711 45819 Z= 0.264 Chirality : 0.042 0.425 4926 Planarity : 0.004 0.054 6102 Dihedral : 4.272 21.782 4647 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.94 % Allowed : 10.52 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4200 helix: 0.82 (0.27), residues: 426 sheet: 0.47 (0.14), residues: 1431 loop : -0.48 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 182 TYR 0.015 0.001 TYR B 131 PHE 0.011 0.001 PHE B 117 TRP 0.021 0.001 TRP G 343 HIS 0.005 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (33645) covalent geometry : angle 0.51237 / 0.26 (45783) hydrogen bonds : bond 0.03107 / 2.11 ( 698) hydrogen bonds : angle 4.82642 / 3.30 ( 1818) metal coordination : bond 0.00845 / 0.50 ( 12) metal coordination : angle 6.10288 / 3.80 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 126 time to evaluate : 1.156 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: I 5 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8071 (mt-10) REVERT: I 14 ASP cc_start: 0.9239 (t0) cc_final: 0.9001 (t0) REVERT: I 45 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8706 (mm-30) REVERT: I 82 GLU cc_start: 0.8386 (mp0) cc_final: 0.7995 (mp0) REVERT: J 117 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: J 185 MET cc_start: 0.8782 (mtm) cc_final: 0.8140 (mtm) REVERT: B 26 LEU cc_start: 0.5896 (OUTLIER) cc_final: 0.5687 (pp) REVERT: B 65 GLN cc_start: 0.8413 (tt0) cc_final: 0.7113 (tm130) REVERT: B 91 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8633 (tp30) REVERT: B 113 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8197 (tm-30) REVERT: H 162 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.8021 (mmtm) REVERT: R 5 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7856 (mt-10) REVERT: R 10 ASP cc_start: 0.8548 (p0) cc_final: 0.7899 (p0) REVERT: R 45 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8584 (mm-30) REVERT: R 63 ASP cc_start: 0.9122 (t0) cc_final: 0.8731 (t0) REVERT: R 82 GLU cc_start: 0.8282 (mp0) cc_final: 0.8043 (mp0) REVERT: C 10 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7629 (t70) REVERT: C 45 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8458 (mt-10) REVERT: T 117 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: T 185 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8422 (mmm) REVERT: N 400 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8116 (ttm-80) REVERT: N 506 ASP cc_start: 0.8574 (t0) cc_final: 0.8260 (OUTLIER) REVERT: N 519 ARG cc_start: 0.8618 (mtm110) cc_final: 0.8407 (mtm110) REVERT: E 4 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6622 (tm) REVERT: E 65 GLN cc_start: 0.8365 (tt0) cc_final: 0.8114 (tt0) REVERT: E 91 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8432 (tp30) REVERT: E 113 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8138 (tm-30) REVERT: E 129 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7153 (tm-30) REVERT: P 48 CYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7020 (t) REVERT: P 82 LEU cc_start: 0.9573 (tp) cc_final: 0.9187 (pp) REVERT: P 88 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8671 (mmtm) REVERT: P 137 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.5856 (m-80) REVERT: S 63 ASP cc_start: 0.8974 (t0) cc_final: 0.8706 (t0) REVERT: O 343 TRP cc_start: 0.8435 (OUTLIER) cc_final: 0.8163 (t60) REVERT: K 65 GLN cc_start: 0.8389 (tt0) cc_final: 0.7051 (tm-30) REVERT: K 91 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8572 (tp30) REVERT: K 113 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8186 (tm-30) REVERT: Q 61 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8097 (ptp-110) REVERT: Q 137 PHE cc_start: 0.6001 (OUTLIER) cc_final: 0.5266 (m-80) outliers start: 67 outliers final: 30 residues processed: 179 average time/residue: 0.7079 time to fit residues: 150.1924 Evaluate side-chains 161 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 117 GLN Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain T residue 30 MET Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 88 LYS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 137 PHE Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain U residue 191 ASN Chi-restraints excluded: chain U residue 193 VAL Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 205 MET Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 343 TRP Chi-restraints excluded: chain O residue 435 ILE Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 95 LYS Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 137 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [23, 138, 386, 353, 112, 14, 292, 159, 218, 70, 262] chunk 23 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 386 optimal weight: 10.0000 chunk 353 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 292 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 218 optimal weight: 0.1980 chunk 70 optimal weight: 6.9990 chunk 262 optimal weight: 40.0000 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 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 = 0.3851 r_free = 0.3851 target = 0.079097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.057019 restraints weight = 109920.389| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.53 r_work: 0.3196 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33657 Z= 0.177 Angle : 0.555 11.864 45819 Z= 0.272 Chirality : 0.042 0.284 4926 Planarity : 0.004 0.055 6102 Dihedral : 4.288 21.850 4647 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.65 % Allowed : 11.30 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 4200 helix: 0.85 (0.27), residues: 426 sheet: 0.47 (0.14), residues: 1422 loop : -0.54 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 81 TYR 0.016 0.001 TYR B 131 PHE 0.010 0.001 PHE B 117 TRP 0.025 0.001 TRP N 343 HIS 0.005 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (33645) covalent geometry : angle 0.52702 / 0.27 (45783) hydrogen bonds : bond 0.03206 / 2.16 ( 698) hydrogen bonds : angle 4.81614 / 3.29 ( 1818) metal coordination : bond 0.01060 / 0.62 ( 12) metal coordination : angle 6.20449 / 3.89 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 120 time to evaluate : 1.238 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: I 5 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7786 (mt-10) REVERT: I 14 ASP cc_start: 0.9227 (t0) cc_final: 0.8963 (t0) REVERT: I 45 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8712 (mm-30) REVERT: I 82 GLU cc_start: 0.8417 (mp0) cc_final: 0.7948 (mp0) REVERT: J 117 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: J 185 MET cc_start: 0.8770 (mtm) cc_final: 0.8339 (mtm) REVERT: B 65 GLN cc_start: 0.8412 (tt0) cc_final: 0.7203 (tm-30) REVERT: B 91 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8718 (tp30) REVERT: B 113 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8189 (tm-30) REVERT: H 87 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7455 (mp0) REVERT: R 5 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7850 (mt-10) REVERT: R 10 ASP cc_start: 0.8557 (p0) cc_final: 0.7908 (p0) REVERT: R 45 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8590 (mm-30) REVERT: R 63 ASP cc_start: 0.9122 (t0) cc_final: 0.8785 (t0) REVERT: R 82 GLU cc_start: 0.8307 (mp0) cc_final: 0.8083 (mp0) REVERT: C 10 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7623 (t70) REVERT: C 45 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8456 (mt-10) REVERT: T 117 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: T 185 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8426 (mmm) REVERT: N 400 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8137 (ttm-80) REVERT: N 506 ASP cc_start: 0.8595 (t0) cc_final: 0.8283 (OUTLIER) REVERT: N 519 ARG cc_start: 0.8685 (mtm110) cc_final: 0.8465 (mtm110) REVERT: E 4 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6650 (tm) REVERT: E 65 GLN cc_start: 0.8362 (tt0) cc_final: 0.8116 (tt0) REVERT: E 91 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8550 (tp30) REVERT: E 113 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8140 (tm-30) REVERT: E 129 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7173 (tm-30) REVERT: P 48 CYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7044 (t) REVERT: P 88 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8665 (mmtm) REVERT: P 137 PHE cc_start: 0.6459 (OUTLIER) cc_final: 0.5958 (m-80) REVERT: S 82 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8263 (mp0) REVERT: O 343 TRP cc_start: 0.8496 (OUTLIER) cc_final: 0.8230 (t60) REVERT: K 65 GLN cc_start: 0.8380 (tt0) cc_final: 0.7046 (tm-30) REVERT: K 91 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8646 (tp30) REVERT: K 113 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8168 (tm-30) REVERT: Q 137 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.5285 (m-80) REVERT: Q 158 LYS cc_start: 0.8717 (tmmm) cc_final: 0.8415 (tmmt) outliers start: 57 outliers final: 29 residues processed: 163 average time/residue: 0.6915 time to fit residues: 133.8115 Evaluate side-chains 156 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 117 GLN Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 311 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain T residue 30 MET Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain P residue 48 CYS Chi-restraints excluded: chain P residue 88 LYS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 137 PHE Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain U residue 191 ASN Chi-restraints excluded: chain U residue 193 VAL Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 205 MET Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 343 TRP Chi-restraints excluded: chain O residue 506 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 95 LYS Chi-restraints excluded: chain Q residue 137 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [116, 208, 152, 159, 316, 76, 143, 131, 146, 254, 242] chunk 116 optimal weight: 30.0000 chunk 208 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 254 optimal weight: 20.0000 chunk 242 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 155 GLN ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.078123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.056041 restraints weight = 110371.447| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.52 r_work: 0.3173 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 33657 Z= 0.235 Angle : 0.596 12.702 45819 Z= 0.293 Chirality : 0.043 0.246 4926 Planarity : 0.004 0.056 6102 Dihedral : 4.470 22.783 4647 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.65 % Allowed : 11.45 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4200 helix: 0.84 (0.28), residues: 408 sheet: 0.46 (0.14), residues: 1437 loop : -0.63 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 123 TYR 0.014 0.001 TYR N 284 PHE 0.012 0.001 PHE H 126 TRP 0.029 0.001 TRP G 343 HIS 0.006 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (33645) covalent geometry : angle 0.56688 / 0.29 (45783) hydrogen bonds : bond 0.03582 / 2.41 ( 698) hydrogen bonds : angle 4.94283 / 3.37 ( 1818) metal coordination : bond 0.01578 / 0.95 ( 12) metal coordination : angle 6.57047 / 4.19 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 117 time to evaluate : 1.181 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: I 45 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8734 (mm-30) REVERT: I 82 GLU cc_start: 0.8362 (mp0) cc_final: 0.7994 (mp0) REVERT: J 185 MET cc_start: 0.8794 (mtm) cc_final: 0.8308 (mtm) REVERT: B 65 GLN cc_start: 0.8376 (tt0) cc_final: 0.7206 (tm-30) REVERT: B 91 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8774 (tp30) REVERT: B 113 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8206 (tm-30) REVERT: H 87 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7477 (mp0) REVERT: R 5 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7824 (mt-10) REVERT: R 63 ASP cc_start: 0.9142 (t0) cc_final: 0.8885 (t0) REVERT: R 82 GLU cc_start: 0.8369 (mp0) cc_final: 0.8009 (mp0) REVERT: C 10 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7603 (t70) REVERT: C 45 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8470 (mt-10) REVERT: T 117 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: T 185 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8432 (mmm) REVERT: N 400 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8123 (ttm-80) REVERT: N 506 ASP cc_start: 0.8631 (t0) cc_final: 0.8324 (OUTLIER) REVERT: N 519 ARG cc_start: 0.8728 (mtm110) cc_final: 0.8503 (mtm110) REVERT: E 4 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6692 (tm) REVERT: E 45 GLU cc_start: 0.9239 (pm20) cc_final: 0.8871 (tm-30) REVERT: E 65 GLN cc_start: 0.8365 (tt0) cc_final: 0.8142 (tt0) REVERT: E 91 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8677 (tp30) REVERT: E 113 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8153 (tm-30) REVERT: E 129 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7303 (tm-30) REVERT: S 63 ASP cc_start: 0.8989 (t0) cc_final: 0.8744 (t0) REVERT: O 343 TRP cc_start: 0.8539 (OUTLIER) cc_final: 0.8263 (t60) REVERT: K 65 GLN cc_start: 0.8316 (tt0) cc_final: 0.7063 (tm-30) REVERT: K 91 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8758 (tp30) REVERT: K 113 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8143 (tm-30) REVERT: Q 137 PHE cc_start: 0.6329 (OUTLIER) cc_final: 0.5509 (m-80) REVERT: Q 158 LYS cc_start: 0.8702 (tmmm) cc_final: 0.8354 (tmmt) outliers start: 57 outliers final: 30 residues processed: 161 average time/residue: 0.7180 time to fit residues: 137.8609 Evaluate side-chains 150 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 311 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain T residue 30 MET Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain P residue 88 LYS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain U residue 191 ASN Chi-restraints excluded: chain U residue 193 VAL Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 205 MET Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 343 TRP Chi-restraints excluded: chain O residue 506 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 95 LYS Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 137 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [403, 343, 303, 314, 82, 79, 257, 395, 10, 131, 67] chunk 403 optimal weight: 10.0000 chunk 343 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 257 optimal weight: 50.0000 chunk 395 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.080173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.058024 restraints weight = 108535.840| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.72 r_work: 0.3201 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33657 Z= 0.135 Angle : 0.542 12.382 45819 Z= 0.264 Chirality : 0.042 0.263 4926 Planarity : 0.004 0.052 6102 Dihedral : 4.205 21.616 4647 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.13 % Allowed : 11.91 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4200 helix: 0.92 (0.27), residues: 426 sheet: 0.54 (0.14), residues: 1353 loop : -0.61 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 182 TYR 0.014 0.001 TYR B 131 PHE 0.010 0.001 PHE O 353 TRP 0.033 0.001 TRP G 343 HIS 0.004 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (33645) covalent geometry : angle 0.51309 / 0.26 (45783) hydrogen bonds : bond 0.02943 / 1.98 ( 698) hydrogen bonds : angle 4.72307 / 3.22 ( 1818) metal coordination : bond 0.00616 / 0.36 ( 12) metal coordination : angle 6.25335 / 3.90 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 1.070 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: I 5 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7774 (mt-10) REVERT: I 45 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8709 (mm-30) REVERT: I 82 GLU cc_start: 0.8347 (mp0) cc_final: 0.7948 (mp0) REVERT: J 117 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: J 185 MET cc_start: 0.8812 (mtm) cc_final: 0.8375 (mtm) REVERT: B 65 GLN cc_start: 0.8354 (tt0) cc_final: 0.7185 (tm-30) REVERT: B 91 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8810 (tp30) REVERT: B 113 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8261 (tm-30) REVERT: H 137 PHE cc_start: 0.6539 (OUTLIER) cc_final: 0.5784 (m-80) REVERT: R 5 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7848 (mt-10) REVERT: R 10 ASP cc_start: 0.8577 (p0) cc_final: 0.7853 (p0) REVERT: R 63 ASP cc_start: 0.9140 (t0) cc_final: 0.8867 (t0) REVERT: R 82 GLU cc_start: 0.8227 (mp0) cc_final: 0.7834 (mp0) REVERT: C 10 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7552 (t70) REVERT: C 45 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8524 (mt-10) REVERT: T 117 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: T 185 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8398 (mmm) REVERT: N 400 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8861 (ttm170) REVERT: N 506 ASP cc_start: 0.8609 (t0) cc_final: 0.8302 (OUTLIER) REVERT: E 4 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6626 (tm) REVERT: E 45 GLU cc_start: 0.9300 (pm20) cc_final: 0.8867 (tm-30) REVERT: E 65 GLN cc_start: 0.8322 (tt0) cc_final: 0.8095 (tt0) REVERT: E 91 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8717 (tp30) REVERT: E 95 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7371 (pttp) REVERT: E 113 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8139 (tm-30) REVERT: E 129 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7223 (tm-30) REVERT: P 88 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8686 (mmtm) REVERT: S 63 ASP cc_start: 0.9008 (t0) cc_final: 0.8777 (t0) REVERT: O 343 TRP cc_start: 0.8453 (OUTLIER) cc_final: 0.8161 (t60) REVERT: K 65 GLN cc_start: 0.8288 (tt0) cc_final: 0.6939 (tm-30) REVERT: K 91 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8783 (tp30) REVERT: K 113 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8114 (tm-30) REVERT: Q 137 PHE cc_start: 0.6025 (OUTLIER) cc_final: 0.5298 (m-80) outliers start: 39 outliers final: 22 residues processed: 148 average time/residue: 0.7295 time to fit residues: 128.3097 Evaluate side-chains 145 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 117 GLN Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain T residue 30 MET Chi-restraints excluded: chain T residue 77 ILE Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 185 MET Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 204 THR Chi-restraints excluded: chain N residue 400 ARG Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain P residue 88 LYS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain U residue 193 VAL Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 205 MET Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 343 TRP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain K residue 95 LYS Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 137 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: [303, 339, 266, 261, 192, 100, 18, 382, 9, 347, 341] chunk 303 optimal weight: 0.9990 chunk 339 optimal weight: 10.0000 chunk 266 optimal weight: 30.0000 chunk 261 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 382 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 347 optimal weight: 9.9990 chunk 341 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 585 ASN ** 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 = 0.3888 r_free = 0.3888 target = 0.079259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.056887 restraints weight = 109241.413| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.72 r_work: 0.3192 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33657 Z= 0.176 Angle : 0.563 12.206 45819 Z= 0.275 Chirality : 0.042 0.242 4926 Planarity : 0.004 0.054 6102 Dihedral : 4.260 21.911 4647 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.30 % Allowed : 11.77 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4200 helix: 0.87 (0.27), residues: 429 sheet: 0.66 (0.14), residues: 1341 loop : -0.68 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG N 519 TYR 0.013 0.001 TYR B 131 PHE 0.010 0.001 PHE O 353 TRP 0.033 0.001 TRP G 343 HIS 0.005 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (33645) covalent geometry : angle 0.53517 / 0.27 (45783) hydrogen bonds : bond 0.03207 / 2.16 ( 698) hydrogen bonds : angle 4.76735 / 3.25 ( 1818) metal coordination : bond 0.01095 / 0.64 ( 12) metal coordination : angle 6.29444 / 3.97 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8444.01 seconds wall clock time: 144 minutes 36.62 seconds (8676.62 seconds total)