Starting phenix.real_space_refine on Tue Sep 15 13:23:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25vf_80403/09_2026/25vf_80403.cif Found real_map, /net/cci-nas-00/data/ceres_data/25vf_80403/09_2026/25vf_80403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25vf_80403/09_2026/25vf_80403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25vf_80403/09_2026/25vf_80403.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25vf_80403/09_2026/25vf_80403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25vf_80403/09_2026/25vf_80403.map" } resolution = 2.29 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= -0.001 sd= 0.128 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 108 5.16 5 C 24531 2.51 5 N 7059 2.21 5 O 7494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 131 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39204 Number of models: 1 Model: "" Number of chains: 27 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: "2" 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: "6" 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: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 877 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "7" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 218} Chain: "A" Number of atoms: 6309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6309 Classifications: {'peptide': 816} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 768} Chain: "5" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 249 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "9" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 506 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} 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: "C" 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: "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: "E" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 877 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 218} Chain: "G" Number of atoms: 6309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6309 Classifications: {'peptide': 816} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 768} Chain: "H" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 249 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "I" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 506 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "J" 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: "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: "L" 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: "M" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 877 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "N" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 218} Chain: "O" Number of atoms: 6309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6309 Classifications: {'peptide': 816} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 768} Chain: "P" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 249 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "Q" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 506 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 6, 'TRANS': 63} Chain: "7" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "N" 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 5614 SG CYS 7 178 53.538 23.617 126.627 1.00 10.66 S ATOM 5784 SG CYS 7 201 60.138 23.369 126.105 1.00 14.00 S ATOM 5502 SG CYS 7 165 57.013 29.023 125.924 1.00 4.53 S ATOM 5830 SG CYS 7 208 56.559 24.999 121.137 1.00 3.78 S ATOM 18674 SG CYS F 178 38.593 91.796 126.579 1.00 8.91 S ATOM 18844 SG CYS F 201 35.125 86.131 126.154 1.00 14.19 S ATOM 18562 SG CYS F 165 41.542 86.107 125.959 1.00 6.38 S ATOM 18890 SG CYS F 208 38.255 88.505 121.131 1.00 6.21 S ATOM 31734 SG CYS N 178 105.119 70.698 126.617 1.00 7.40 S ATOM 31904 SG CYS N 201 101.937 76.523 126.131 1.00 13.29 S ATOM 31622 SG CYS N 165 98.695 71.006 125.950 1.00 5.12 S ATOM 31950 SG CYS N 208 102.342 72.597 121.137 1.00 0.85 S Time building chain proxies: 8.69, per 1000 atoms: 0.22 Number of scatterers: 39204 At special positions: 0 Unit cell: (125.936, 121.306, 260.206, 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 108 16.00 O 7494 8.00 N 7059 7.00 C 24531 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: 3.53 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 7 301 " pdb="FE4 SF4 7 301 " - pdb=" SG CYS 7 208 " pdb="FE1 SF4 7 301 " - pdb=" SG CYS 7 178 " pdb="FE2 SF4 7 301 " - pdb=" SG CYS 7 201 " pdb="FE3 SF4 7 301 " - pdb=" SG CYS 7 165 " pdb=" SF4 F 301 " pdb="FE2 SF4 F 301 " - pdb=" SG CYS F 201 " pdb="FE4 SF4 F 301 " - pdb=" SG CYS F 208 " pdb="FE1 SF4 F 301 " - pdb=" SG CYS F 178 " pdb="FE3 SF4 F 301 " - pdb=" SG CYS F 165 " pdb=" SF4 N 301 " pdb="FE2 SF4 N 301 " - pdb=" SG CYS N 201 " pdb="FE4 SF4 N 301 " - pdb=" SG CYS N 208 " pdb="FE3 SF4 N 301 " - pdb=" SG CYS N 165 " pdb="FE1 SF4 N 301 " - pdb=" SG CYS N 178 " Number of angles added : 36 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9144 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 79 sheets defined 14.9% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.748A pdb=" N VAL b 80 " --> pdb=" O LEU b 76 " (cutoff:3.500A) Processing helix chain '2' and resid 76 through 88 removed outlier: 3.866A pdb=" N VAL 2 80 " --> pdb=" O LEU 2 76 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS 2 88 " --> pdb=" O GLN 2 84 " (cutoff:3.500A) Processing helix chain '6' and resid 55 through 69 Proline residue: 6 60 - end of helix Processing helix chain 'c' and resid 55 through 68 Proline residue: c 60 - end of helix Processing helix chain '7' and resid 2 through 9 removed outlier: 3.743A pdb=" N GLN 7 8 " --> pdb=" O THR 7 4 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA 7 9 " --> pdb=" O ALA 7 5 " (cutoff:3.500A) Processing helix chain '7' and resid 24 through 27 removed outlier: 3.524A pdb=" N GLY 7 27 " --> pdb=" O THR 7 24 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 24 through 27' Processing helix chain '7' and resid 79 through 88 Processing helix chain '7' and resid 89 through 92 removed outlier: 3.894A pdb=" N VAL 7 92 " --> pdb=" O ASP 7 89 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 89 through 92' Processing helix chain '7' and resid 104 through 106 No H-bonds generated for 'chain '7' and resid 104 through 106' Processing helix chain '7' and resid 107 through 111 Processing helix chain '7' and resid 147 through 151 removed outlier: 3.781A pdb=" N PHE 7 151 " --> pdb=" O PRO 7 148 " (cutoff:3.500A) Processing helix chain '7' and resid 165 through 170 Processing helix chain '7' and resid 195 through 199 Processing helix chain '7' and resid 204 through 213 removed outlier: 3.582A pdb=" N ARG 7 211 " --> pdb=" O ASP 7 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.886A pdb=" N LEU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 removed outlier: 3.658A pdb=" N ILE A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.642A pdb=" N THR A 383 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 416 removed outlier: 3.685A pdb=" N GLY A 416 " --> pdb=" O PRO A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 426 through 434 removed outlier: 3.681A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 465 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 597 through 604 removed outlier: 4.160A pdb=" N ALA A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain '5' and resid 580 through 599 Processing helix chain '5' and resid 604 through 611 Processing helix chain '9' and resid 137 through 143 Processing helix chain '9' and resid 198 through 200 No H-bonds generated for 'chain '9' and resid 198 through 200' Processing helix chain 'B' and resid 76 through 88 removed outlier: 3.764A pdb=" N VAL B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 88 removed outlier: 3.908A pdb=" N VAL C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 87 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 88 " --> pdb=" O GLN C 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 69 Proline residue: D 60 - end of helix Processing helix chain 'E' and resid 55 through 69 Proline residue: E 60 - end of helix Processing helix chain 'F' and resid 2 through 8 removed outlier: 3.659A pdb=" N GLN F 8 " --> pdb=" O THR F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 27 removed outlier: 3.518A pdb=" N GLY F 27 " --> pdb=" O THR F 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 24 through 27' Processing helix chain 'F' and resid 79 through 88 Processing helix chain 'F' and resid 89 through 92 removed outlier: 3.915A pdb=" N VAL F 92 " --> pdb=" O ASP F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 92' Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 147 through 151 removed outlier: 3.727A pdb=" N PHE F 151 " --> pdb=" O PRO F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 195 through 199 Processing helix chain 'F' and resid 204 through 213 removed outlier: 3.565A pdb=" N ARG F 211 " --> pdb=" O ASP F 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 289 Processing helix chain 'G' and resid 299 through 303 Processing helix chain 'G' and resid 304 through 316 removed outlier: 3.844A pdb=" N LEU G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 353 removed outlier: 3.676A pdb=" N ILE G 352 " --> pdb=" O ASP G 348 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 383 removed outlier: 3.551A pdb=" N THR G 383 " --> pdb=" O PRO G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 416 removed outlier: 3.631A pdb=" N GLY G 416 " --> pdb=" O PRO G 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 413 through 416' Processing helix chain 'G' and resid 426 through 434 removed outlier: 3.721A 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 478 Processing helix chain 'G' and resid 490 through 495 Processing helix chain 'G' and resid 597 through 604 removed outlier: 4.183A pdb=" N ALA G 601 " --> pdb=" O SER G 597 " (cutoff:3.500A) Processing helix chain 'H' and resid 580 through 600 Processing helix chain 'H' and resid 604 through 611 Processing helix chain 'I' and resid 137 through 143 Processing helix chain 'I' and resid 198 through 200 No H-bonds generated for 'chain 'I' and resid 198 through 200' Processing helix chain 'J' and resid 76 through 88 removed outlier: 3.742A pdb=" N VAL J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS J 88 " --> pdb=" O GLN J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 88 removed outlier: 3.882A pdb=" N VAL K 80 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS K 88 " --> pdb=" O GLN K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 69 Proline residue: L 60 - end of helix Processing helix chain 'M' and resid 55 through 69 Proline residue: M 60 - end of helix Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 24 through 27 removed outlier: 3.573A pdb=" N GLY N 27 " --> pdb=" O THR N 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 24 through 27' Processing helix chain 'N' and resid 79 through 88 Processing helix chain 'N' and resid 89 through 92 removed outlier: 3.966A pdb=" N VAL N 92 " --> pdb=" O ASP N 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 89 through 92' Processing helix chain 'N' and resid 104 through 106 No H-bonds generated for 'chain 'N' and resid 104 through 106' Processing helix chain 'N' and resid 107 through 111 Processing helix chain 'N' and resid 147 through 151 removed outlier: 3.765A pdb=" N PHE N 151 " --> pdb=" O PRO N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 170 Processing helix chain 'N' and resid 195 through 199 Processing helix chain 'N' and resid 204 through 213 removed outlier: 3.583A pdb=" N ARG N 211 " --> pdb=" O ASP N 207 " (cutoff:3.500A) Processing helix chain 'O' and resid 278 through 289 Processing helix chain 'O' and resid 299 through 303 Processing helix chain 'O' and resid 304 through 316 removed outlier: 3.916A pdb=" N LEU O 308 " --> pdb=" O ASP O 304 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 353 removed outlier: 3.665A pdb=" N ILE O 352 " --> pdb=" O ASP O 348 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE O 353 " --> pdb=" O LEU O 349 " (cutoff:3.500A) Processing helix chain 'O' and resid 379 through 383 removed outlier: 3.633A pdb=" N THR O 383 " --> pdb=" O PRO O 380 " (cutoff:3.500A) Processing helix chain 'O' and resid 398 through 402 Processing helix chain 'O' and resid 413 through 416 removed outlier: 3.808A pdb=" N GLY O 416 " --> pdb=" O PRO O 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 413 through 416' Processing helix chain 'O' and resid 426 through 434 removed outlier: 3.695A pdb=" N ARG O 432 " --> pdb=" O ARG O 428 " (cutoff:3.500A) Processing helix chain 'O' and resid 447 through 465 Processing helix chain 'O' and resid 474 through 478 Processing helix chain 'O' and resid 490 through 495 Processing helix chain 'O' and resid 597 through 604 removed outlier: 4.133A pdb=" N ALA O 601 " --> pdb=" O SER O 597 " (cutoff:3.500A) Processing helix chain 'P' and resid 580 through 600 Processing helix chain 'P' and resid 604 through 611 Processing helix chain 'Q' and resid 137 through 143 removed outlier: 3.616A pdb=" N MET Q 141 " --> pdb=" O GLY Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 198 through 200 No H-bonds generated for 'chain 'Q' and resid 198 through 200' Processing sheet with id=AA1, first strand: chain 'b' and resid 9 through 14 removed outlier: 4.632A 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: 6.546A pdb=" N THR b 150 " --> pdb=" O SER b 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 41 through 45 removed outlier: 4.235A pdb=" N ASP b 42 " --> pdb=" O GLY b 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 109 through 110 removed outlier: 4.122A pdb=" N THR b 109 " --> pdb=" O VAL b 118 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL b 118 " --> pdb=" O THR b 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain '2' and resid 9 through 14 removed outlier: 4.276A pdb=" N ILE 2 10 " --> pdb=" O ILE 2 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '2' and resid 24 through 28 current: chain '2' and resid 65 through 70 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 65 through 70 current: chain '2' and resid 125 through 134 removed outlier: 5.636A pdb=" N VAL 2 132 " --> pdb=" O GLN 2 152 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN 2 152 " --> pdb=" O VAL 2 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 41 through 45 removed outlier: 4.472A pdb=" N ASP 2 42 " --> pdb=" O GLY 2 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 109 through 110 Processing sheet with id=AA7, first strand: chain '6' and resid 16 through 21 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 43 through 54 current: chain '6' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 83 through 87 current: chain '6' and resid 100 through 110 WARNING: can't find start of bonding for strands! previous: chain '6' 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 110 WARNING: can't find start of bonding for strands! previous: chain 'c' 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 110 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 100 through 110 current: chain 'E' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 43 through 54 current: chain 'E' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 83 through 87 current: chain 'E' and resid 100 through 110 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 100 through 110 current: chain 'L' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 43 through 54 current: chain 'L' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 83 through 87 current: chain 'L' and resid 100 through 110 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 100 through 110 current: chain 'M' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 43 through 54 current: chain 'M' and resid 83 through 87 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 83 through 87 current: chain 'M' and resid 100 through 110 Processing sheet with id=AA8, first strand: chain '6' and resid 24 through 27 removed outlier: 7.855A pdb=" N LEU 7 15 " --> pdb=" O ALA 6 35 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY 6 37 " --> pdb=" O LEU 7 15 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ARG 7 17 " --> pdb=" O GLY 6 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '7' and resid 30 through 34 current: chain '7' and resid 47 through 51 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 47 through 51 current: chain '7' and resid 71 through 75 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 71 through 75 current: chain '7' and resid 124 through 136 removed outlier: 6.298A pdb=" N GLU 7 131 " --> pdb=" O SER 7 146 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N SER 7 146 " --> pdb=" O GLU 7 131 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LYS 7 133 " --> pdb=" O GLU 7 144 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU 7 144 " --> pdb=" O LYS 7 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 23 through 26 Processing sheet with id=AB1, first strand: chain '7' and resid 155 through 156 Processing sheet with id=AB2, first strand: chain 'A' and resid 71 through 75 removed outlier: 6.465A pdb=" N ALA A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG A 30 " --> pdb=" O ILE Q 194 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE Q 194 " --> pdb=" O ARG A 30 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS A 32 " --> pdb=" O ALA Q 192 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA Q 192 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A 34 " --> pdb=" O ILE Q 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AB4, first strand: chain 'A' and resid 88 through 100 removed outlier: 4.583A pdb=" N VAL A 90 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU A 208 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 98 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG A 206 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL A 207 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER A 123 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 209 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 106 through 110 removed outlier: 6.303A pdb=" N ILE A 147 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU A 156 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL A 149 " --> pdb=" O TRP A 154 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TRP A 154 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AB7, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AB8, first strand: chain 'A' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AC1, first strand: chain 'A' and resid 334 through 336 Processing sheet with id=AC2, first strand: chain 'A' and resid 355 through 359 Processing sheet with id=AC3, first strand: chain 'A' and resid 374 through 378 removed outlier: 6.673A pdb=" N ILE A 485 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR A 376 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 590 " --> pdb=" O MET A 577 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 579 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU A 588 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP A 467 " --> pdb=" O GLN A 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 419 through 425 Processing sheet with id=AC5, first strand: chain 'A' and resid 499 through 506 removed outlier: 3.513A pdb=" N ALA A 504 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 541 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER A 547 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN A 561 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 628 through 635 Processing sheet with id=AC7, first strand: chain 'A' and resid 654 through 663 removed outlier: 6.343A pdb=" N TYR A 657 " --> pdb=" O ARG A 673 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG A 673 " --> pdb=" O TYR A 657 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA A 659 " --> pdb=" O VAL A 671 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 669 through 674 current: chain 'A' and resid 706 through 707 Processing sheet with id=AC8, first strand: chain 'A' and resid 725 through 731 removed outlier: 3.660A pdb=" N TYR A 725 " --> pdb=" O GLY A 740 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 768 through 774 removed outlier: 6.675A pdb=" N ILE A 754 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 772 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR A 752 " --> pdb=" O LEU A 772 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA A 774 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA A 750 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '9' and resid 178 through 180 Processing sheet with id=AD2, first strand: chain '9' and resid 183 through 185 Processing sheet with id=AD3, first strand: chain '9' and resid 188 through 196 removed outlier: 6.578A pdb=" N LEU G 34 " --> pdb=" O ILE 9 190 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA 9 192 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS G 32 " --> pdb=" O ALA 9 192 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE 9 194 " --> pdb=" O ARG G 30 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG G 30 " --> pdb=" O ILE 9 194 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA G 224 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 9 through 14 removed outlier: 4.706A 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: 6.544A pdb=" N THR B 150 " --> pdb=" O SER B 133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 41 through 45 removed outlier: 4.217A pdb=" N ASP B 42 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 109 through 110 removed outlier: 3.865A pdb=" N THR B 109 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 118 " --> pdb=" O THR B 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 9 through 14 removed outlier: 4.287A pdb=" N ILE C 10 " --> pdb=" O ILE C 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 24 through 28 current: chain 'C' and resid 65 through 70 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 65 through 70 current: chain 'C' and resid 125 through 134 removed outlier: 6.638A pdb=" N THR C 150 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 41 through 45 removed outlier: 4.754A pdb=" N ASP C 42 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 109 through 110 Processing sheet with id=AE1, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.944A pdb=" N LEU F 15 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY D 37 " --> pdb=" O LEU F 15 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ARG F 17 " --> pdb=" O GLY D 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 30 through 34 current: chain 'F' and resid 47 through 51 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 47 through 51 current: chain 'F' and resid 71 through 75 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 71 through 75 current: chain 'F' and resid 124 through 136 removed outlier: 6.276A pdb=" N GLU F 131 " --> pdb=" O SER F 146 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N SER F 146 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS F 133 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU F 144 " --> pdb=" O LYS F 133 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 23 through 26 Processing sheet with id=AE3, first strand: chain 'F' and resid 155 through 156 Processing sheet with id=AE4, first strand: chain 'G' and resid 88 through 100 removed outlier: 4.578A pdb=" N VAL G 90 " --> pdb=" O ILE G 214 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU G 208 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL G 98 " --> pdb=" O ARG G 206 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG G 206 " --> pdb=" O VAL G 98 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL G 207 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER G 123 " --> pdb=" O VAL G 207 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA G 209 " --> pdb=" O ARG G 121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 106 through 110 removed outlier: 6.301A pdb=" N ILE G 147 " --> pdb=" O GLU G 156 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU G 156 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL G 149 " --> pdb=" O TRP G 154 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N TRP G 154 " --> pdb=" O VAL G 149 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 136 through 137 Processing sheet with id=AE7, first strand: chain 'G' and resid 250 through 253 Processing sheet with id=AE8, first strand: chain 'G' and resid 256 through 257 Processing sheet with id=AE9, first strand: chain 'G' and resid 318 through 320 Processing sheet with id=AF1, first strand: chain 'G' and resid 355 through 359 Processing sheet with id=AF2, first strand: chain 'G' and resid 374 through 378 removed outlier: 6.684A pdb=" N ILE G 485 " --> pdb=" O GLU G 374 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR G 376 " --> pdb=" O ILE G 485 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR G 590 " --> pdb=" O MET G 577 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE G 579 " --> pdb=" O GLU G 588 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU G 588 " --> pdb=" O ILE G 579 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP G 467 " --> pdb=" O GLN G 593 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 419 through 425 removed outlier: 6.709A pdb=" N LEU G 405 " --> pdb=" O LEU G 438 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE G 440 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU G 407 " --> pdb=" O ILE G 440 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 499 through 506 removed outlier: 3.541A pdb=" N ALA G 504 " --> pdb=" O THR G 511 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL G 545 " --> pdb=" O VAL G 541 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL G 541 " --> pdb=" O VAL G 545 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER G 547 " --> pdb=" O GLN G 539 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLN G 561 " --> pdb=" O ASN G 527 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 628 through 635 removed outlier: 6.529A pdb=" N THR G 642 " --> pdb=" O GLY G 683 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 654 through 663 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 669 through 670 current: chain 'G' and resid 706 through 707 Processing sheet with id=AF7, first strand: chain 'G' and resid 725 through 731 removed outlier: 3.612A pdb=" N TYR G 725 " --> pdb=" O GLY G 740 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 768 through 774 removed outlier: 6.645A pdb=" N ILE G 754 " --> pdb=" O LEU G 770 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU G 772 " --> pdb=" O THR G 752 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR G 752 " --> pdb=" O LEU G 772 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA G 774 " --> pdb=" O ALA G 750 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA G 750 " --> pdb=" O ALA G 774 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 178 through 180 Processing sheet with id=AG1, first strand: chain 'I' and resid 183 through 185 Processing sheet with id=AG2, first strand: chain 'I' and resid 188 through 196 removed outlier: 6.553A pdb=" N LEU O 34 " --> pdb=" O ILE I 190 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA I 192 " --> pdb=" O LYS O 32 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS O 32 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE I 194 " --> pdb=" O ARG O 30 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG O 30 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA O 224 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 9 through 14 removed outlier: 4.637A pdb=" N ILE J 10 " --> pdb=" O ILE J 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 24 through 28 current: chain 'J' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 65 through 71 current: chain 'J' and resid 125 through 134 removed outlier: 6.546A pdb=" N THR J 150 " --> pdb=" O SER J 133 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 41 through 45 removed outlier: 4.070A pdb=" N ASP J 42 " --> pdb=" O GLY J 59 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 109 through 110 removed outlier: 4.250A pdb=" N THR J 109 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL J 118 " --> pdb=" O THR J 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'K' and resid 9 through 14 removed outlier: 4.335A 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 70 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 65 through 70 current: chain 'K' and resid 125 through 134 removed outlier: 5.736A pdb=" N VAL K 132 " --> pdb=" O GLN K 152 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLN K 152 " --> pdb=" O VAL K 132 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 41 through 45 removed outlier: 4.653A pdb=" N ASP K 42 " --> pdb=" O GLY K 59 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 109 through 110 Processing sheet with id=AG9, first strand: chain 'L' and resid 24 through 27 removed outlier: 7.892A pdb=" N LEU N 15 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY L 37 " --> pdb=" O LEU N 15 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ARG N 17 " --> pdb=" O GLY L 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 30 through 34 current: chain 'N' and resid 47 through 51 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 47 through 51 current: chain 'N' and resid 71 through 75 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 71 through 75 current: chain 'N' and resid 124 through 136 removed outlier: 6.452A pdb=" N GLU N 131 " --> pdb=" O SER N 146 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N SER N 146 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS N 133 " --> pdb=" O GLU N 144 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU N 144 " --> pdb=" O LYS N 133 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 23 through 26 Processing sheet with id=AH2, first strand: chain 'N' and resid 155 through 156 Processing sheet with id=AH3, first strand: chain 'O' and resid 88 through 100 removed outlier: 4.588A pdb=" N VAL O 90 " --> pdb=" O ILE O 214 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU O 208 " --> pdb=" O VAL O 96 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL O 98 " --> pdb=" O ARG O 206 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ARG O 206 " --> pdb=" O VAL O 98 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL O 207 " --> pdb=" O SER O 123 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER O 123 " --> pdb=" O VAL O 207 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA O 209 " --> pdb=" O ARG O 121 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 106 through 110 removed outlier: 6.334A pdb=" N ILE O 147 " --> pdb=" O GLU O 156 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU O 156 " --> pdb=" O ILE O 147 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL O 149 " --> pdb=" O TRP O 154 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TRP O 154 " --> pdb=" O VAL O 149 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 136 through 137 Processing sheet with id=AH6, first strand: chain 'O' and resid 250 through 253 Processing sheet with id=AH7, first strand: chain 'O' and resid 256 through 257 Processing sheet with id=AH8, first strand: chain 'O' and resid 318 through 320 Processing sheet with id=AH9, first strand: chain 'O' and resid 355 through 359 Processing sheet with id=AI1, first strand: chain 'O' and resid 374 through 378 removed outlier: 6.682A pdb=" N ILE O 485 " --> pdb=" O GLU O 374 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR O 376 " --> pdb=" O ILE O 485 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR O 590 " --> pdb=" O MET O 577 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE O 579 " --> pdb=" O GLU O 588 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU O 588 " --> pdb=" O ILE O 579 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASP O 467 " --> pdb=" O GLN O 593 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 419 through 425 removed outlier: 6.711A pdb=" N LEU O 405 " --> pdb=" O LEU O 438 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE O 440 " --> pdb=" O LEU O 405 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU O 407 " --> pdb=" O ILE O 440 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 499 through 506 removed outlier: 3.568A pdb=" N ALA O 504 " --> pdb=" O THR O 511 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL O 545 " --> pdb=" O VAL O 541 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL O 541 " --> pdb=" O VAL O 545 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER O 547 " --> pdb=" O GLN O 539 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLN O 561 " --> pdb=" O ASN O 527 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'O' and resid 628 through 635 removed outlier: 6.706A pdb=" N THR O 642 " --> pdb=" O GLY O 683 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'O' and resid 654 through 663 removed outlier: 6.366A pdb=" N TYR O 657 " --> pdb=" O ARG O 673 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG O 673 " --> pdb=" O TYR O 657 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA O 659 " --> pdb=" O VAL O 671 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 669 through 674 current: chain 'O' and resid 706 through 707 Processing sheet with id=AI6, first strand: chain 'O' and resid 725 through 731 removed outlier: 3.582A pdb=" N TYR O 725 " --> pdb=" O GLY O 740 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'O' and resid 767 through 774 removed outlier: 6.675A pdb=" N ILE O 754 " --> pdb=" O LEU O 770 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU O 772 " --> pdb=" O THR O 752 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR O 752 " --> pdb=" O LEU O 772 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA O 774 " --> pdb=" O ALA O 750 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA O 750 " --> pdb=" O ALA O 774 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2655 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: 10.51 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 17659 1.44 - 1.65: 22283 1.65 - 1.86: 153 1.86 - 2.07: 0 2.07 - 2.28: 36 Bond restraints: 40131 Sorted by residual: bond pdb=" CG PRO A 719 " pdb=" CD PRO A 719 " ideal model delta sigma weight residual 1.503 1.392 0.111 3.40e-02 8.65e+02 1.06e+01 bond pdb=" CB PRO N 196 " pdb=" CG PRO N 196 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.72e+00 bond pdb=" CB PRO F 196 " pdb=" CG PRO F 196 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.19e+00 bond pdb=" CB PRO A 719 " pdb=" CG PRO A 719 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.90e+00 bond pdb=" CB PRO 7 196 " pdb=" CG PRO 7 196 " ideal model delta sigma weight residual 1.492 1.558 -0.066 5.00e-02 4.00e+02 1.76e+00 ... (remaining 40126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 53634 1.88 - 3.77: 868 3.77 - 5.65: 87 5.65 - 7.54: 17 7.54 - 9.42: 6 Bond angle restraints: 54612 Sorted by residual: angle pdb=" CA PRO N 196 " pdb=" N PRO N 196 " pdb=" CD PRO N 196 " ideal model delta sigma weight residual 112.00 102.58 9.42 1.40e+00 5.10e-01 4.53e+01 angle pdb=" N PRO A 719 " pdb=" CD PRO A 719 " pdb=" CG PRO A 719 " ideal model delta sigma weight residual 103.20 94.07 9.13 1.50e+00 4.44e-01 3.70e+01 angle pdb=" CA PRO F 196 " pdb=" N PRO F 196 " pdb=" CD PRO F 196 " ideal model delta sigma weight residual 112.00 104.52 7.48 1.40e+00 5.10e-01 2.85e+01 angle pdb=" CA PRO A 719 " pdb=" N PRO A 719 " pdb=" CD PRO A 719 " ideal model delta sigma weight residual 112.00 105.30 6.70 1.40e+00 5.10e-01 2.29e+01 angle pdb=" C PHE B 83 " pdb=" N GLN B 84 " pdb=" CA GLN B 84 " ideal model delta sigma weight residual 121.14 113.71 7.43 1.75e+00 3.27e-01 1.80e+01 ... (remaining 54607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 20853 17.97 - 35.94: 2060 35.94 - 53.91: 583 53.91 - 71.88: 115 71.88 - 89.85: 83 Dihedral angle restraints: 23694 sinusoidal: 9345 harmonic: 14349 Sorted by residual: dihedral pdb=" CA HIS G 83 " pdb=" C HIS G 83 " pdb=" N ILE G 84 " pdb=" CA ILE G 84 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA HIS O 83 " pdb=" C HIS O 83 " pdb=" N ILE O 84 " pdb=" CA ILE O 84 " ideal model delta harmonic sigma weight residual 180.00 155.36 24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA HIS A 83 " pdb=" C HIS A 83 " pdb=" N ILE A 84 " pdb=" CA ILE A 84 " ideal model delta harmonic sigma weight residual 180.00 156.59 23.41 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 23691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3715 0.033 - 0.067: 1435 0.067 - 0.100: 442 0.100 - 0.133: 269 0.133 - 0.167: 16 Chirality restraints: 5877 Sorted by residual: chirality pdb=" CA ASP b 105 " pdb=" N ASP b 105 " pdb=" C ASP b 105 " pdb=" CB ASP b 105 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE b 151 " pdb=" N ILE b 151 " pdb=" C ILE b 151 " pdb=" CB ILE b 151 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE J 151 " pdb=" N ILE J 151 " pdb=" C ILE J 151 " pdb=" CB ILE J 151 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 5874 not shown) Planarity restraints: 7272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP N 195 " -0.083 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO N 196 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO N 196 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO N 196 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 195 " -0.065 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO F 196 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO F 196 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 196 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 7 195 " -0.055 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO 7 196 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO 7 196 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO 7 196 " -0.046 5.00e-02 4.00e+02 ... (remaining 7269 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 744 2.68 - 3.23: 35502 3.23 - 3.79: 63654 3.79 - 4.34: 89100 4.34 - 4.90: 142846 Nonbonded interactions: 331846 Sorted by model distance: nonbonded pdb=" O THR J 5 " pdb=" OG1 THR J 8 " model vdw 2.124 3.040 nonbonded pdb=" O ARG O 246 " pdb=" NE1 TRP O 275 " model vdw 2.153 3.120 nonbonded pdb=" O GLN c 89 " pdb=" NE2 GLN L 21 " model vdw 2.158 3.120 nonbonded pdb=" O GLN 6 89 " pdb=" NE2 GLN c 21 " model vdw 2.166 3.120 nonbonded pdb=" NE2 GLN 6 21 " pdb=" O GLN E 89 " model vdw 2.168 3.120 ... (remaining 331841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain '2' selection = chain 'B' selection = chain 'C' selection = chain 'J' selection = chain 'K' selection = chain 'b' } ncs_group { reference = chain '5' selection = chain 'H' selection = chain 'P' } ncs_group { reference = (chain '6' and resid 4 through 113) selection = (chain 'D' and resid 4 through 113) selection = chain 'E' selection = (chain 'L' and resid 4 through 113) selection = chain 'M' selection = chain 'c' } ncs_group { reference = chain '7' selection = chain 'F' selection = chain 'N' } ncs_group { reference = chain '9' selection = chain 'I' selection = chain 'Q' } ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 10.360 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: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 44.590 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.150 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 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 : 0.003 0.130 40143 Z= 0.121 Angle : 0.590 9.419 54648 Z= 0.323 Chirality : 0.044 0.167 5877 Planarity : 0.005 0.120 7272 Dihedral : 16.627 89.847 14550 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.85 % Favored : 96.91 % Rotamer: Outliers : 2.49 % Allowed : 19.08 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.02 (0.11), residues: 5046 helix: 0.66 (0.22), residues: 558 sheet: 0.74 (0.12), residues: 1632 loop : -0.58 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 75 TYR 0.012 0.001 TYR I 161 PHE 0.013 0.001 PHE D 74 TRP 0.018 0.001 TRP G 283 HIS 0.003 0.001 HIS O 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (40131) covalent geometry : angle 0.58412 / 0.32 (54612) hydrogen bonds : bond 0.13753 / 9.31 ( 1005) hydrogen bonds : angle 6.64944 / 4.63 ( 2655) metal coordination : bond 0.00228 / 0.16 ( 12) metal coordination : angle 3.15284 / 1.92 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 498 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 7 1 MET cc_start: 0.3315 (tpp) cc_final: 0.2830 (ptt) REVERT: G 81 GLN cc_start: 0.7988 (mt0) cc_final: 0.7596 (mt0) REVERT: J 61 ARG cc_start: 0.7934 (ptp-170) cc_final: 0.7241 (mtm180) REVERT: N 29 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7405 (pm20) outliers start: 102 outliers final: 80 residues processed: 589 average time/residue: 0.8726 time to fit residues: 606.2686 Evaluate side-chains 561 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 480 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 87 GLU Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain 2 residue 14 VAL Chi-restraints excluded: chain 2 residue 93 SER Chi-restraints excluded: chain 2 residue 139 PHE Chi-restraints excluded: chain 2 residue 147 THR Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain 7 residue 126 ASN Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 229 VAL Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 728 CYS Chi-restraints excluded: chain 9 residue 191 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 425 ASN Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 551 SER Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 693 VAL Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 142 ASN Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 14 LYS Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 64 SER Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain O residue 294 LEU Chi-restraints excluded: chain O residue 425 ASN Chi-restraints excluded: chain O residue 492 VAL Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 614 THR Chi-restraints excluded: chain O residue 728 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 0.4980 chunk 494 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.9024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 104 ASN 7 39 GLN 7 179 ASN A 92 ASN A 418 GLN C 43 GLN D 18 GLN F 39 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 GLN F 179 ASN G 92 ASN G 259 GLN M 92 GLN N 39 GLN O 92 ASN O 755 GLN O 780 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.160895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118384 restraints weight = 37963.918| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.82 r_work: 0.3165 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 40143 Z= 0.173 Angle : 0.630 8.397 54648 Z= 0.330 Chirality : 0.046 0.205 5877 Planarity : 0.005 0.066 7272 Dihedral : 6.380 73.171 5684 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.91 % Favored : 96.85 % Rotamer: Outliers : 3.39 % Allowed : 17.59 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.09 (0.11), residues: 5046 helix: 0.60 (0.22), residues: 573 sheet: 0.68 (0.13), residues: 1611 loop : -0.62 (0.11), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 30 TYR 0.014 0.002 TYR O 284 PHE 0.015 0.002 PHE D 74 TRP 0.018 0.002 TRP A 281 HIS 0.008 0.001 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (40131) covalent geometry : angle 0.62206 / 0.33 (54612) hydrogen bonds : bond 0.04446 / 2.98 ( 1005) hydrogen bonds : angle 5.85697 / 4.05 ( 2655) metal coordination : bond 0.01055 / 0.70 ( 12) metal coordination : angle 3.94516 / 2.37 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 493 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 80 VAL cc_start: 0.6709 (t) cc_final: 0.6500 (m) REVERT: c 112 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8138 (p0) REVERT: 7 29 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: A 81 GLN cc_start: 0.8301 (mt0) cc_final: 0.8083 (mt0) REVERT: A 294 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8885 (mm) REVERT: A 437 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: E 48 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8415 (mp10) REVERT: F 169 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8554 (mp) REVERT: G 81 GLN cc_start: 0.8115 (mt0) cc_final: 0.7891 (mt0) REVERT: G 169 ARG cc_start: 0.8494 (ptm-80) cc_final: 0.8199 (ttt-90) REVERT: G 728 CYS cc_start: 0.5845 (OUTLIER) cc_final: 0.5533 (m) REVERT: G 734 ARG cc_start: 0.4336 (OUTLIER) cc_final: 0.3921 (ttm110) REVERT: I 133 MET cc_start: 0.7467 (mmm) cc_final: 0.7062 (mmm) REVERT: K 138 ASP cc_start: 0.4964 (OUTLIER) cc_final: 0.4706 (p0) REVERT: M 18 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8400 (tt0) REVERT: M 48 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8202 (mt0) REVERT: N 87 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8117 (m-80) REVERT: O 244 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8358 (tp30) REVERT: O 439 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8030 (mt-10) outliers start: 139 outliers final: 69 residues processed: 585 average time/residue: 0.8782 time to fit residues: 605.9940 Evaluate side-chains 566 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 483 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain 2 residue 94 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 139 PHE Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 112 ASN Chi-restraints excluded: chain 7 residue 29 GLU Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 229 VAL Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 693 VAL Chi-restraints excluded: chain G residue 728 CYS Chi-restraints excluded: chain G residue 734 ARG Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 48 GLN Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 294 LEU Chi-restraints excluded: chain O residue 439 GLU Chi-restraints excluded: chain O residue 492 VAL Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 614 THR Chi-restraints excluded: chain O residue 635 VAL Chi-restraints excluded: chain Q residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 176 optimal weight: 10.0000 chunk 396 optimal weight: 1.9990 chunk 341 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 465 optimal weight: 1.9990 chunk 330 optimal weight: 5.9990 chunk 324 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 48 GLN c 104 ASN 7 39 GLN 7 179 ASN A 92 ASN A 755 GLN A 780 HIS C 43 GLN D 18 GLN D 48 GLN F 39 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN G 92 ASN G 259 GLN M 92 GLN N 39 GLN O 81 GLN O 92 ASN O 259 GLN O 530 ASN P 594 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.158288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116439 restraints weight = 37784.832| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.68 r_work: 0.3122 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 40143 Z= 0.286 Angle : 0.761 8.920 54648 Z= 0.403 Chirality : 0.052 0.284 5877 Planarity : 0.006 0.058 7272 Dihedral : 6.609 59.530 5628 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.49 % Favored : 96.27 % Rotamer: Outliers : 4.73 % Allowed : 16.40 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.11), residues: 5046 helix: 0.11 (0.21), residues: 573 sheet: 0.48 (0.12), residues: 1641 loop : -0.84 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 219 TYR 0.020 0.003 TYR O 284 PHE 0.021 0.003 PHE 6 111 TRP 0.021 0.002 TRP A 281 HIS 0.011 0.002 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.29 (40131) covalent geometry : angle 0.75400 / 0.40 (54612) hydrogen bonds : bond 0.05493 / 3.66 ( 1005) hydrogen bonds : angle 6.09455 / 4.22 ( 2655) metal coordination : bond 0.01884 / 1.30 ( 12) metal coordination : angle 4.13564 / 2.44 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 476 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 4 LEU cc_start: 0.5754 (mm) cc_final: 0.5284 (tm) REVERT: 6 18 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: c 18 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8566 (tp40) REVERT: c 87 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8546 (mtm180) REVERT: c 112 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8156 (p0) REVERT: 7 29 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: 7 87 PHE cc_start: 0.8577 (m-80) cc_final: 0.8372 (t80) REVERT: A 121 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8433 (ttm-80) REVERT: A 182 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7647 (mmm-85) REVERT: A 437 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: A 510 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8885 (mt) REVERT: 5 587 MET cc_start: 0.8093 (mtp) cc_final: 0.7831 (mtm) REVERT: B 61 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7902 (mtt90) REVERT: E 48 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8377 (mt0) REVERT: F 87 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.8277 (m-80) REVERT: F 169 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8624 (mp) REVERT: G 81 GLN cc_start: 0.8264 (mt0) cc_final: 0.7996 (mt0) REVERT: G 510 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8903 (mt) REVERT: G 573 ARG cc_start: 0.8962 (mtp180) cc_final: 0.8752 (mtp180) REVERT: G 728 CYS cc_start: 0.5816 (OUTLIER) cc_final: 0.5539 (m) REVERT: I 133 MET cc_start: 0.7517 (mmm) cc_final: 0.7135 (mmm) REVERT: J 95 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.5699 (mptt) REVERT: K 138 ASP cc_start: 0.5102 (OUTLIER) cc_final: 0.4887 (p0) REVERT: M 18 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8400 (tt0) REVERT: M 48 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: M 112 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8177 (p0) REVERT: N 87 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8171 (m-80) REVERT: N 126 ASN cc_start: 0.9322 (OUTLIER) cc_final: 0.8632 (t0) REVERT: N 231 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7322 (ptt) REVERT: O 244 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8334 (tp30) REVERT: O 439 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8175 (mt-10) outliers start: 194 outliers final: 99 residues processed: 615 average time/residue: 0.8693 time to fit residues: 632.1546 Evaluate side-chains 588 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 464 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain b residue 91 GLU Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain 2 residue 58 LYS Chi-restraints excluded: chain 2 residue 94 VAL Chi-restraints excluded: chain 2 residue 110 VAL Chi-restraints excluded: chain 2 residue 139 PHE Chi-restraints excluded: chain 2 residue 143 THR Chi-restraints excluded: chain 2 residue 147 THR Chi-restraints excluded: chain 6 residue 18 GLN Chi-restraints excluded: chain 6 residue 92 GLN Chi-restraints excluded: chain c residue 18 GLN Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 87 ARG Chi-restraints excluded: chain c residue 112 ASN Chi-restraints excluded: chain 7 residue 29 GLU Chi-restraints excluded: chain 7 residue 82 SER Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 229 VAL Chi-restraints excluded: chain 7 residue 231 MET Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain 5 residue 610 VAL Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 87 PHE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 510 LEU Chi-restraints excluded: chain G residue 532 LYS Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 693 VAL Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 728 CYS Chi-restraints excluded: chain G residue 779 THR Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain I residue 199 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 95 LYS Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 48 GLN Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 126 ASN Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 73 GLU Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 294 LEU Chi-restraints excluded: chain O residue 424 VAL Chi-restraints excluded: chain O residue 439 GLU Chi-restraints excluded: chain O residue 492 VAL Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 614 THR Chi-restraints excluded: chain O residue 635 VAL Chi-restraints excluded: chain O residue 690 LEU Chi-restraints excluded: chain O residue 779 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 106 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 486 optimal weight: 9.9990 chunk 473 optimal weight: 0.7980 chunk 458 optimal weight: 5.9990 chunk 474 optimal weight: 0.0070 chunk 247 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 491 optimal weight: 1.9990 chunk 226 optimal weight: 8.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 48 GLN c 104 ASN 7 39 GLN A 92 ASN A 530 ASN A 755 GLN C 43 GLN D 18 GLN D 48 GLN E 112 ASN F 39 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN G 92 ASN G 259 GLN M 92 GLN O 92 ASN O 259 GLN O 561 GLN O 755 GLN P 594 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.159692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117690 restraints weight = 37634.516| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.69 r_work: 0.3128 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 40143 Z= 0.185 Angle : 0.645 9.043 54648 Z= 0.340 Chirality : 0.047 0.233 5877 Planarity : 0.005 0.054 7272 Dihedral : 6.275 58.643 5625 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.01 % Favored : 96.77 % Rotamer: Outliers : 4.37 % Allowed : 17.06 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.36 (0.11), residues: 5046 helix: 0.41 (0.22), residues: 573 sheet: 0.47 (0.12), residues: 1647 loop : -0.80 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 200 TYR 0.015 0.002 TYR 2 131 PHE 0.016 0.002 PHE D 74 TRP 0.024 0.002 TRP 2 125 HIS 0.008 0.001 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (40131) covalent geometry : angle 0.63774 / 0.34 (54612) hydrogen bonds : bond 0.04467 / 2.99 ( 1005) hydrogen bonds : angle 5.84513 / 4.05 ( 2655) metal coordination : bond 0.01021 / 0.70 ( 12) metal coordination : angle 3.75626 / 2.22 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 475 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 3 ILE cc_start: 0.4479 (OUTLIER) cc_final: 0.3905 (pp) REVERT: 6 18 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: c 18 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8592 (tp40) REVERT: c 112 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8124 (p0) REVERT: 7 29 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7248 (pm20) REVERT: A 81 GLN cc_start: 0.8412 (mt0) cc_final: 0.8158 (mt0) REVERT: A 130 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: A 437 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: 5 587 MET cc_start: 0.8038 (mtp) cc_final: 0.7770 (mtm) REVERT: B 61 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7825 (mtt90) REVERT: E 48 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8400 (mp10) REVERT: E 62 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8928 (mtp-110) REVERT: F 169 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8574 (mp) REVERT: G 81 GLN cc_start: 0.8085 (mt0) cc_final: 0.7805 (mt0) REVERT: G 610 LEU cc_start: 0.5426 (OUTLIER) cc_final: 0.5018 (mt) REVERT: G 728 CYS cc_start: 0.5885 (OUTLIER) cc_final: 0.5620 (m) REVERT: G 734 ARG cc_start: 0.4383 (OUTLIER) cc_final: 0.3622 (ttm110) REVERT: G 735 ILE cc_start: 0.5614 (OUTLIER) cc_final: 0.5338 (mm) REVERT: I 133 MET cc_start: 0.7471 (mmm) cc_final: 0.7131 (mmm) REVERT: K 138 ASP cc_start: 0.5065 (OUTLIER) cc_final: 0.3133 (t70) REVERT: M 18 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: M 48 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: N 87 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: N 231 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7717 (ptm) REVERT: O 244 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8363 (tp30) REVERT: O 439 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: Q 147 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8669 (mtpt) outliers start: 179 outliers final: 88 residues processed: 596 average time/residue: 0.8871 time to fit residues: 624.3821 Evaluate side-chains 585 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 474 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain 2 residue 94 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 139 PHE Chi-restraints excluded: chain 2 residue 147 THR Chi-restraints excluded: chain 6 residue 13 ILE Chi-restraints excluded: chain 6 residue 18 GLN Chi-restraints excluded: chain 6 residue 92 GLN Chi-restraints excluded: chain c residue 18 GLN Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 112 ASN Chi-restraints excluded: chain 7 residue 29 GLU Chi-restraints excluded: chain 7 residue 82 SER Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 229 VAL Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 693 VAL Chi-restraints excluded: chain G residue 728 CYS Chi-restraints excluded: chain G residue 734 ARG Chi-restraints excluded: chain G residue 735 ILE Chi-restraints excluded: chain G residue 779 THR Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain I residue 199 ARG Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 48 GLN Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 294 LEU Chi-restraints excluded: chain O residue 424 VAL Chi-restraints excluded: chain O residue 439 GLU Chi-restraints excluded: chain O residue 492 VAL Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 614 THR Chi-restraints excluded: chain O residue 633 THR Chi-restraints excluded: chain O residue 690 LEU Chi-restraints excluded: chain O residue 779 THR Chi-restraints excluded: chain Q residue 147 LYS Chi-restraints excluded: chain Q residue 200 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 305 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 480 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 436 optimal weight: 2.9990 chunk 481 optimal weight: 6.9990 chunk 467 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 48 GLN c 104 ASN 7 39 GLN 7 179 ASN A 92 ASN A 755 GLN C 43 GLN D 18 GLN D 48 GLN F 39 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN G 92 ASN G 259 GLN M 92 GLN N 39 GLN O 92 ASN P 594 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.159337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117581 restraints weight = 37549.130| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.63 r_work: 0.3138 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40143 Z= 0.200 Angle : 0.661 8.595 54648 Z= 0.348 Chirality : 0.048 0.236 5877 Planarity : 0.005 0.055 7272 Dihedral : 6.277 59.851 5621 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.35 % Favored : 96.43 % Rotamer: Outliers : 4.37 % Allowed : 17.11 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.38 (0.11), residues: 5046 helix: 0.41 (0.21), residues: 573 sheet: 0.46 (0.12), residues: 1641 loop : -0.81 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 200 TYR 0.016 0.002 TYR Q 195 PHE 0.017 0.002 PHE D 74 TRP 0.018 0.002 TRP A 281 HIS 0.009 0.002 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (40131) covalent geometry : angle 0.65340 / 0.35 (54612) hydrogen bonds : bond 0.04616 / 3.09 ( 1005) hydrogen bonds : angle 5.83505 / 4.04 ( 2655) metal coordination : bond 0.01167 / 0.80 ( 12) metal coordination : angle 3.85960 / 2.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 480 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 3 ILE cc_start: 0.4357 (OUTLIER) cc_final: 0.3758 (pp) REVERT: b 91 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5645 (mm-30) REVERT: 6 18 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8402 (tt0) REVERT: c 18 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8577 (tp40) REVERT: c 62 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8880 (mtp-110) REVERT: c 92 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8664 (mp-120) REVERT: c 112 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8073 (p0) REVERT: 7 29 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: 7 215 ASP cc_start: 0.8491 (m-30) cc_final: 0.8237 (m-30) REVERT: A 81 GLN cc_start: 0.8476 (mt0) cc_final: 0.8239 (mt0) REVERT: A 130 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: A 437 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: 5 587 MET cc_start: 0.8056 (mtp) cc_final: 0.7791 (mtm) REVERT: B 61 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7834 (mtt90) REVERT: E 48 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8387 (mp10) REVERT: E 62 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8922 (mtp-110) REVERT: F 169 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8575 (mp) REVERT: G 81 GLN cc_start: 0.8121 (mt0) cc_final: 0.7853 (mt0) REVERT: G 339 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8186 (mtm180) REVERT: G 728 CYS cc_start: 0.5783 (OUTLIER) cc_final: 0.5440 (m) REVERT: G 734 ARG cc_start: 0.4301 (OUTLIER) cc_final: 0.3724 (ttm110) REVERT: I 133 MET cc_start: 0.7446 (mmm) cc_final: 0.7142 (mmm) REVERT: K 138 ASP cc_start: 0.5084 (OUTLIER) cc_final: 0.3101 (m-30) REVERT: L 62 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8763 (mtp-110) REVERT: M 18 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: M 48 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8176 (mt0) REVERT: N 87 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: N 231 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7742 (ptt) REVERT: O 244 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8323 (tp30) REVERT: O 439 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: P 587 MET cc_start: 0.8189 (mtp) cc_final: 0.7989 (mtm) REVERT: Q 147 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8696 (mtpt) outliers start: 179 outliers final: 95 residues processed: 604 average time/residue: 0.8823 time to fit residues: 629.3082 Evaluate side-chains 593 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 472 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 91 GLU Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain 2 residue 94 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 143 THR Chi-restraints excluded: chain 2 residue 147 THR Chi-restraints excluded: chain 6 residue 13 ILE Chi-restraints excluded: chain 6 residue 18 GLN Chi-restraints excluded: chain 6 residue 92 GLN Chi-restraints excluded: chain c residue 18 GLN Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 62 ARG Chi-restraints excluded: chain c residue 92 GLN Chi-restraints excluded: chain c residue 112 ASN Chi-restraints excluded: chain 7 residue 29 GLU Chi-restraints excluded: chain 7 residue 82 SER Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 229 VAL Chi-restraints excluded: chain 7 residue 231 MET Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 339 ARG Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 693 VAL Chi-restraints excluded: chain G residue 728 CYS Chi-restraints excluded: chain G residue 734 ARG Chi-restraints excluded: chain G residue 779 THR Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain I residue 199 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 44 SER Chi-restraints excluded: chain M residue 48 GLN Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 84 ILE Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 294 LEU Chi-restraints excluded: chain O residue 424 VAL Chi-restraints excluded: chain O residue 439 GLU Chi-restraints excluded: chain O residue 492 VAL Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 614 THR Chi-restraints excluded: chain O residue 690 LEU Chi-restraints excluded: chain O residue 779 THR Chi-restraints excluded: chain O residue 791 LEU Chi-restraints excluded: chain Q residue 147 LYS Chi-restraints excluded: chain Q residue 200 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 10 optimal weight: 0.7980 chunk 291 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 432 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 442 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 246 optimal weight: 0.3980 chunk 170 optimal weight: 30.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 43 GLN c 48 GLN c 104 ASN 7 39 GLN 7 179 ASN A 92 ASN A 755 GLN C 43 GLN D 18 GLN D 48 GLN F 39 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN G 92 ASN J 79 HIS M 92 GLN N 39 GLN O 92 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.155714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.115755 restraints weight = 37612.742| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.80 r_work: 0.3075 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40143 Z= 0.165 Angle : 0.619 8.418 54648 Z= 0.325 Chirality : 0.046 0.199 5877 Planarity : 0.005 0.053 7272 Dihedral : 6.090 58.549 5617 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.97 % Favored : 96.81 % Rotamer: Outliers : 4.12 % Allowed : 17.25 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.29 (0.11), residues: 5046 helix: 0.66 (0.22), residues: 567 sheet: 0.51 (0.12), residues: 1629 loop : -0.79 (0.11), residues: 2850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 200 TYR 0.016 0.002 TYR A 775 PHE 0.015 0.002 PHE D 74 TRP 0.017 0.002 TRP A 281 HIS 0.007 0.001 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (40131) covalent geometry : angle 0.61237 / 0.33 (54612) hydrogen bonds : bond 0.04205 / 2.82 ( 1005) hydrogen bonds : angle 5.71262 / 3.95 ( 2655) metal coordination : bond 0.00865 / 0.59 ( 12) metal coordination : angle 3.66849 / 2.17 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 486 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 3 ILE cc_start: 0.4301 (OUTLIER) cc_final: 0.3674 (pp) REVERT: 6 18 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8306 (tp40) REVERT: c 18 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8630 (tp40) REVERT: c 62 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8874 (mtp-110) REVERT: c 92 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8650 (mp-120) REVERT: 7 29 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7189 (pm20) REVERT: A 130 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: A 182 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7619 (mmm-85) REVERT: A 200 ARG cc_start: 0.7705 (mmt90) cc_final: 0.7437 (mmm-85) REVERT: A 437 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: B 55 LYS cc_start: 0.6884 (pttt) cc_final: 0.5998 (mmtm) REVERT: E 62 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8899 (mtp-110) REVERT: F 62 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.6879 (mmp80) REVERT: F 169 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8531 (mp) REVERT: F 172 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: F 231 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7350 (ptm) REVERT: G 339 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8073 (mtm180) REVERT: G 610 LEU cc_start: 0.5501 (OUTLIER) cc_final: 0.5110 (mt) REVERT: G 728 CYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5598 (m) REVERT: G 734 ARG cc_start: 0.4419 (OUTLIER) cc_final: 0.3819 (ttm110) REVERT: I 133 MET cc_start: 0.7391 (mmm) cc_final: 0.7095 (mmm) REVERT: K 138 ASP cc_start: 0.5032 (OUTLIER) cc_final: 0.3064 (m-30) REVERT: M 18 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: M 48 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8188 (mt0) REVERT: N 231 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7865 (ptm) REVERT: O 244 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8291 (tp30) REVERT: O 439 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: O 688 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7974 (mtp85) REVERT: P 587 MET cc_start: 0.8117 (mtp) cc_final: 0.7917 (mtm) outliers start: 169 outliers final: 96 residues processed: 604 average time/residue: 0.8795 time to fit residues: 629.7909 Evaluate side-chains 601 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 480 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain 2 residue 94 VAL Chi-restraints excluded: chain 2 residue 143 THR Chi-restraints excluded: chain 2 residue 147 THR Chi-restraints excluded: chain 6 residue 13 ILE Chi-restraints excluded: chain 6 residue 18 GLN Chi-restraints excluded: chain c residue 18 GLN Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 62 ARG Chi-restraints excluded: chain c residue 92 GLN Chi-restraints excluded: chain 7 residue 29 GLU Chi-restraints excluded: chain 7 residue 82 SER Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 229 VAL Chi-restraints excluded: chain 7 residue 231 MET Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain 5 residue 610 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 339 ARG Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 693 VAL Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 728 CYS Chi-restraints excluded: chain G residue 734 ARG Chi-restraints excluded: chain G residue 779 THR Chi-restraints excluded: chain G residue 791 LEU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain I residue 199 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 44 SER Chi-restraints excluded: chain M residue 48 GLN Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 84 ILE Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 294 LEU Chi-restraints excluded: chain O residue 424 VAL Chi-restraints excluded: chain O residue 439 GLU Chi-restraints excluded: chain O residue 492 VAL Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 614 THR Chi-restraints excluded: chain O residue 635 VAL Chi-restraints excluded: chain O residue 688 ARG Chi-restraints excluded: chain O residue 791 LEU Chi-restraints excluded: chain Q residue 200 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 415 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 457 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 301 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 9 GLN 2 152 GLN c 48 GLN c 104 ASN ** 7 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 179 ASN A 92 ASN A 755 GLN C 43 GLN D 18 GLN D 48 GLN F 39 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN G 92 ASN J 79 HIS M 92 GLN N 39 GLN O 8 HIS O 92 ASN O 561 GLN P 594 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112486 restraints weight = 37436.296| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.70 r_work: 0.3040 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 40143 Z= 0.333 Angle : 0.798 9.113 54648 Z= 0.424 Chirality : 0.055 0.353 5877 Planarity : 0.007 0.062 7272 Dihedral : 6.722 59.849 5617 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.82 % Favored : 95.94 % Rotamer: Outliers : 4.69 % Allowed : 16.64 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.59 (0.11), residues: 5046 helix: 0.10 (0.21), residues: 561 sheet: 0.36 (0.12), residues: 1623 loop : -0.94 (0.11), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 219 TYR 0.025 0.003 TYR Q 195 PHE 0.024 0.003 PHE 6 111 TRP 0.021 0.003 TRP A 281 HIS 0.012 0.003 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00757 / 0.33 (40131) covalent geometry : angle 0.79131 / 0.42 (54612) hydrogen bonds : bond 0.05620 / 3.74 ( 1005) hydrogen bonds : angle 6.16097 / 4.27 ( 2655) metal coordination : bond 0.02018 / 1.38 ( 12) metal coordination : angle 4.22600 / 2.44 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 494 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 3 ILE cc_start: 0.4291 (OUTLIER) cc_final: 0.3720 (pp) REVERT: b 25 VAL cc_start: 0.7064 (m) cc_final: 0.6850 (t) REVERT: b 61 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7861 (mtt90) REVERT: b 91 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5659 (mm-30) REVERT: 6 18 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: c 18 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8516 (tp40) REVERT: c 62 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8935 (mtp-110) REVERT: c 92 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8624 (mp-120) REVERT: c 112 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8113 (p0) REVERT: 7 29 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: 7 215 ASP cc_start: 0.8459 (m-30) cc_final: 0.8202 (m-30) REVERT: A 130 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: A 132 GLU cc_start: 0.7518 (tp30) cc_final: 0.7245 (tm-30) REVERT: A 182 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7637 (mmm-85) REVERT: A 437 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: 5 587 MET cc_start: 0.8038 (mtp) cc_final: 0.7801 (mtm) REVERT: B 25 VAL cc_start: 0.7247 (m) cc_final: 0.7029 (t) REVERT: B 55 LYS cc_start: 0.7069 (pttt) cc_final: 0.6029 (mmtm) REVERT: B 61 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7923 (mtt90) REVERT: E 48 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: E 62 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8946 (mtp-110) REVERT: F 169 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8604 (mp) REVERT: F 172 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: G 339 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8289 (mtm180) REVERT: G 519 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7446 (mtp-110) REVERT: G 728 CYS cc_start: 0.5794 (OUTLIER) cc_final: 0.5538 (m) REVERT: G 734 ARG cc_start: 0.4358 (OUTLIER) cc_final: 0.3968 (ptt-90) REVERT: I 133 MET cc_start: 0.7385 (mmm) cc_final: 0.7108 (mmm) REVERT: I 199 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7497 (mmp-170) REVERT: J 95 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.5913 (mptt) REVERT: K 27 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5318 (tm-30) REVERT: K 138 ASP cc_start: 0.5237 (OUTLIER) cc_final: 0.3378 (t70) REVERT: L 62 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8815 (mtp-110) REVERT: M 18 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: M 48 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: M 62 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8726 (mtp-110) REVERT: M 112 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8091 (p0) REVERT: N 87 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: N 231 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8008 (ptm) REVERT: O 182 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7474 (mmm-85) REVERT: O 244 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: O 439 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: O 688 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7994 (mtp85) REVERT: P 587 MET cc_start: 0.8106 (mtp) cc_final: 0.7875 (mtm) outliers start: 192 outliers final: 109 residues processed: 621 average time/residue: 0.8841 time to fit residues: 650.1066 Evaluate side-chains 625 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 480 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 61 ARG Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 91 GLU Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain 2 residue 13 LEU Chi-restraints excluded: chain 2 residue 94 VAL Chi-restraints excluded: chain 2 residue 143 THR Chi-restraints excluded: chain 2 residue 147 THR Chi-restraints excluded: chain 6 residue 13 ILE Chi-restraints excluded: chain 6 residue 18 GLN Chi-restraints excluded: chain 6 residue 92 GLN Chi-restraints excluded: chain c residue 18 GLN Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 62 ARG Chi-restraints excluded: chain c residue 92 GLN Chi-restraints excluded: chain c residue 112 ASN Chi-restraints excluded: chain 7 residue 29 GLU Chi-restraints excluded: chain 7 residue 82 SER Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 229 VAL Chi-restraints excluded: chain 7 residue 231 MET Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain 5 residue 610 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 339 ARG Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 519 ARG Chi-restraints excluded: chain G residue 532 LYS Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 693 VAL Chi-restraints excluded: chain G residue 698 VAL Chi-restraints excluded: chain G residue 728 CYS Chi-restraints excluded: chain G residue 734 ARG Chi-restraints excluded: chain G residue 779 THR Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain I residue 199 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 95 LYS Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 27 GLU Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 48 GLN Chi-restraints excluded: chain M residue 62 ARG Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 294 LEU Chi-restraints excluded: chain O residue 424 VAL Chi-restraints excluded: chain O residue 439 GLU Chi-restraints excluded: chain O residue 492 VAL Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 614 THR Chi-restraints excluded: chain O residue 633 THR Chi-restraints excluded: chain O residue 688 ARG Chi-restraints excluded: chain O residue 779 THR Chi-restraints excluded: chain O residue 791 LEU Chi-restraints excluded: chain Q residue 200 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 295 optimal weight: 3.9990 chunk 329 optimal weight: 0.2980 chunk 448 optimal weight: 1.9990 chunk 431 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 252 optimal weight: 0.8980 chunk 422 optimal weight: 7.9990 chunk 166 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 48 GLN c 104 ASN 7 39 GLN 7 179 ASN A 92 ASN A 755 GLN C 43 GLN D 18 GLN F 39 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN G 92 ASN G 561 GLN J 79 HIS M 92 GLN O 92 ASN O 561 GLN O 755 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116666 restraints weight = 37425.004| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.95 r_work: 0.3082 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 40143 Z= 0.135 Angle : 0.598 11.101 54648 Z= 0.313 Chirality : 0.045 0.181 5877 Planarity : 0.005 0.052 7272 Dihedral : 6.070 59.086 5617 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.75 % Favored : 97.03 % Rotamer: Outliers : 3.64 % Allowed : 17.72 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.31 (0.11), residues: 5046 helix: 0.66 (0.22), residues: 567 sheet: 0.48 (0.12), residues: 1629 loop : -0.79 (0.11), residues: 2850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 800 TYR 0.017 0.001 TYR A 775 PHE 0.015 0.001 PHE D 74 TRP 0.026 0.002 TRP C 125 HIS 0.005 0.001 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (40131) covalent geometry : angle 0.59120 / 0.31 (54612) hydrogen bonds : bond 0.03923 / 2.64 ( 1005) hydrogen bonds : angle 5.70915 / 3.95 ( 2655) metal coordination : bond 0.00599 / 0.40 ( 12) metal coordination : angle 3.43353 / 2.04 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 497 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 3 ILE cc_start: 0.4148 (OUTLIER) cc_final: 0.3442 (pp) REVERT: 6 18 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8276 (tp40) REVERT: c 18 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8647 (tp40) REVERT: c 62 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8865 (mtp-110) REVERT: c 92 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8649 (mp-120) REVERT: 7 29 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: A 132 GLU cc_start: 0.7425 (tp30) cc_final: 0.7193 (tm-30) REVERT: A 200 ARG cc_start: 0.7699 (mmt90) cc_final: 0.7436 (mmm-85) REVERT: A 439 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: 5 587 MET cc_start: 0.8034 (mtp) cc_final: 0.7784 (mtm) REVERT: B 55 LYS cc_start: 0.7046 (pttt) cc_final: 0.6104 (mmtm) REVERT: E 62 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8902 (mtp-110) REVERT: F 169 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8490 (mp) REVERT: F 231 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7755 (ptm) REVERT: G 339 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8062 (mtm180) REVERT: G 610 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.5114 (mt) REVERT: G 728 CYS cc_start: 0.5753 (OUTLIER) cc_final: 0.5456 (m) REVERT: G 734 ARG cc_start: 0.4299 (OUTLIER) cc_final: 0.4039 (ppp80) REVERT: I 133 MET cc_start: 0.7399 (mmm) cc_final: 0.7129 (mmm) REVERT: I 199 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7447 (mmp-170) REVERT: K 138 ASP cc_start: 0.5151 (OUTLIER) cc_final: 0.3207 (m-30) REVERT: L 62 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8646 (mtp-110) REVERT: M 18 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8407 (tp40) REVERT: M 48 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: M 62 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8597 (mtp-110) REVERT: N 231 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7949 (ptm) REVERT: O 244 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8312 (tp30) REVERT: O 439 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: O 688 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7962 (mtp85) REVERT: P 587 MET cc_start: 0.8088 (mtp) cc_final: 0.7882 (mtm) outliers start: 149 outliers final: 82 residues processed: 600 average time/residue: 0.9053 time to fit residues: 640.7804 Evaluate side-chains 590 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 484 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain b residue 139 PHE Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain 2 residue 127 THR Chi-restraints excluded: chain 2 residue 143 THR Chi-restraints excluded: chain 2 residue 147 THR Chi-restraints excluded: chain 6 residue 13 ILE Chi-restraints excluded: chain 6 residue 18 GLN Chi-restraints excluded: chain c residue 18 GLN Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 62 ARG Chi-restraints excluded: chain c residue 92 GLN Chi-restraints excluded: chain 7 residue 29 GLU Chi-restraints excluded: chain 7 residue 82 SER Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 229 VAL Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain 5 residue 610 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 339 ARG Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 693 VAL Chi-restraints excluded: chain G residue 728 CYS Chi-restraints excluded: chain G residue 734 ARG Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain I residue 199 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 48 GLN Chi-restraints excluded: chain M residue 62 ARG Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 294 LEU Chi-restraints excluded: chain O residue 439 GLU Chi-restraints excluded: chain O residue 492 VAL Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 614 THR Chi-restraints excluded: chain O residue 688 ARG Chi-restraints excluded: chain O residue 791 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 98 optimal weight: 0.0060 chunk 327 optimal weight: 6.9990 chunk 307 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 477 optimal weight: 6.9990 chunk 382 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 260 optimal weight: 9.9990 chunk 418 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 104 ASN ** 7 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 179 ASN A 92 ASN A 755 GLN C 43 GLN D 18 GLN F 39 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN J 79 HIS M 92 GLN N 39 GLN O 92 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114289 restraints weight = 37614.854| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.79 r_work: 0.3067 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 40143 Z= 0.212 Angle : 0.675 9.675 54648 Z= 0.355 Chirality : 0.048 0.260 5877 Planarity : 0.005 0.054 7272 Dihedral : 6.326 58.606 5617 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.41 % Favored : 96.39 % Rotamer: Outliers : 3.44 % Allowed : 17.79 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.37 (0.11), residues: 5046 helix: 0.48 (0.22), residues: 567 sheet: 0.47 (0.12), residues: 1617 loop : -0.82 (0.11), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 800 TYR 0.021 0.002 TYR Q 195 PHE 0.018 0.002 PHE G 353 TRP 0.019 0.002 TRP A 281 HIS 0.010 0.002 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (40131) covalent geometry : angle 0.66753 / 0.36 (54612) hydrogen bonds : bond 0.04671 / 3.13 ( 1005) hydrogen bonds : angle 5.86020 / 4.05 ( 2655) metal coordination : bond 0.01234 / 0.85 ( 12) metal coordination : angle 3.90004 / 2.29 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 488 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 3 ILE cc_start: 0.4154 (OUTLIER) cc_final: 0.3528 (pp) REVERT: 6 18 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: c 18 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8511 (tp40) REVERT: c 62 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8867 (mtp-110) REVERT: c 92 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8641 (mp-120) REVERT: 7 29 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7222 (pm20) REVERT: A 132 GLU cc_start: 0.7406 (tp30) cc_final: 0.7190 (tm-30) REVERT: A 200 ARG cc_start: 0.7733 (mmt90) cc_final: 0.7437 (mmm-85) REVERT: A 439 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: 5 587 MET cc_start: 0.7997 (mtp) cc_final: 0.7756 (mtm) REVERT: B 55 LYS cc_start: 0.7251 (pttt) cc_final: 0.6141 (mmtm) REVERT: B 61 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7841 (mtt90) REVERT: C 49 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8720 (mp) REVERT: E 48 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8305 (mp10) REVERT: E 62 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8932 (mtp-110) REVERT: F 169 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8560 (mp) REVERT: F 231 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7843 (ptm) REVERT: G 339 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8103 (mtm180) REVERT: G 610 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5152 (mt) REVERT: G 728 CYS cc_start: 0.5906 (OUTLIER) cc_final: 0.5570 (m) REVERT: G 734 ARG cc_start: 0.4431 (OUTLIER) cc_final: 0.3960 (ptt-90) REVERT: I 133 MET cc_start: 0.7296 (mmm) cc_final: 0.7029 (mmm) REVERT: I 199 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7476 (mmp-170) REVERT: J 95 LYS cc_start: 0.6702 (OUTLIER) cc_final: 0.5980 (mptt) REVERT: K 27 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5317 (tm-30) REVERT: K 138 ASP cc_start: 0.5187 (OUTLIER) cc_final: 0.3265 (m-30) REVERT: L 62 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8754 (mtp-110) REVERT: M 18 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: M 48 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: M 62 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8639 (mtp-110) REVERT: N 87 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8162 (m-80) REVERT: N 231 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7975 (ptm) REVERT: O 244 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8254 (tp30) REVERT: O 439 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8029 (mt-10) REVERT: O 688 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7997 (mtp85) outliers start: 141 outliers final: 86 residues processed: 585 average time/residue: 0.9026 time to fit residues: 622.7644 Evaluate side-chains 594 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 478 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain b residue 139 PHE Chi-restraints excluded: chain 2 residue 13 LEU Chi-restraints excluded: chain 2 residue 127 THR Chi-restraints excluded: chain 2 residue 143 THR Chi-restraints excluded: chain 2 residue 147 THR Chi-restraints excluded: chain 6 residue 13 ILE Chi-restraints excluded: chain 6 residue 18 GLN Chi-restraints excluded: chain 6 residue 92 GLN Chi-restraints excluded: chain c residue 18 GLN Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 62 ARG Chi-restraints excluded: chain c residue 92 GLN Chi-restraints excluded: chain 7 residue 29 GLU Chi-restraints excluded: chain 7 residue 82 SER Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 229 VAL Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain 5 residue 610 VAL Chi-restraints excluded: chain B residue 61 ARG Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 339 ARG Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 693 VAL Chi-restraints excluded: chain G residue 728 CYS Chi-restraints excluded: chain G residue 734 ARG Chi-restraints excluded: chain G residue 779 THR Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain I residue 199 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 95 LYS Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 27 GLU Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 48 GLN Chi-restraints excluded: chain M residue 62 ARG Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 294 LEU Chi-restraints excluded: chain O residue 439 GLU Chi-restraints excluded: chain O residue 492 VAL Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 614 THR Chi-restraints excluded: chain O residue 688 ARG Chi-restraints excluded: chain O residue 779 THR Chi-restraints excluded: chain O residue 791 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 480 optimal weight: 3.9990 chunk 245 optimal weight: 0.7980 chunk 337 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 489 optimal weight: 10.0000 chunk 275 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 486 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 464 optimal weight: 0.0020 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 104 ASN ** 7 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 179 ASN A 92 ASN A 418 GLN A 755 GLN C 43 GLN D 18 GLN F 39 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN G 81 GLN G 92 ASN G 131 GLN J 79 HIS M 92 GLN N 39 GLN O 92 ASN ** O 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116142 restraints weight = 37484.319| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.76 r_work: 0.3094 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40143 Z= 0.139 Angle : 0.601 11.843 54648 Z= 0.314 Chirality : 0.045 0.167 5877 Planarity : 0.005 0.052 7272 Dihedral : 5.998 58.597 5617 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.93 % Favored : 96.87 % Rotamer: Outliers : 2.88 % Allowed : 18.50 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.23 (0.11), residues: 5046 helix: 0.78 (0.22), residues: 567 sheet: 0.54 (0.12), residues: 1617 loop : -0.75 (0.11), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 800 TYR 0.020 0.001 TYR A 775 PHE 0.014 0.001 PHE D 74 TRP 0.018 0.001 TRP C 125 HIS 0.006 0.001 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (40131) covalent geometry : angle 0.59491 / 0.31 (54612) hydrogen bonds : bond 0.03930 / 2.65 ( 1005) hydrogen bonds : angle 5.63526 / 3.90 ( 2655) metal coordination : bond 0.00668 / 0.45 ( 12) metal coordination : angle 3.48960 / 2.07 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10092 Ramachandran restraints generated. 5046 Oldfield, 0 Emsley, 5046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 487 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 3 ILE cc_start: 0.4065 (OUTLIER) cc_final: 0.3462 (pp) REVERT: 2 58 LYS cc_start: 0.8749 (mtpp) cc_final: 0.8257 (mttp) REVERT: 6 18 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8243 (tp40) REVERT: c 18 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8620 (tp40) REVERT: c 62 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8862 (mtp-110) REVERT: c 92 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8626 (mp-120) REVERT: 7 29 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: A 132 GLU cc_start: 0.7399 (tp30) cc_final: 0.7177 (tm-30) REVERT: A 294 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8821 (mm) REVERT: A 439 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: 5 587 MET cc_start: 0.8011 (mtp) cc_final: 0.7765 (mtm) REVERT: B 55 LYS cc_start: 0.7165 (pttt) cc_final: 0.6124 (mmtm) REVERT: E 48 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8282 (mp10) REVERT: E 62 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8898 (mtp-110) REVERT: F 169 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8484 (mp) REVERT: F 231 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7862 (ptm) REVERT: G 339 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8067 (mtm180) REVERT: G 610 LEU cc_start: 0.5511 (OUTLIER) cc_final: 0.5139 (mt) REVERT: G 728 CYS cc_start: 0.5770 (OUTLIER) cc_final: 0.5429 (m) REVERT: G 734 ARG cc_start: 0.4474 (OUTLIER) cc_final: 0.4221 (ppp80) REVERT: I 133 MET cc_start: 0.7268 (mmm) cc_final: 0.7043 (mmm) REVERT: I 199 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7562 (mmp-170) REVERT: J 95 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.5951 (mptt) REVERT: K 138 ASP cc_start: 0.5167 (OUTLIER) cc_final: 0.3265 (m-30) REVERT: L 62 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8772 (mtp-110) REVERT: M 18 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8368 (tp40) REVERT: M 48 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: M 62 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8600 (mtp-110) REVERT: N 231 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7971 (ptm) REVERT: O 244 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8266 (tp30) REVERT: O 439 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: O 688 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7971 (mtp85) outliers start: 118 outliers final: 80 residues processed: 570 average time/residue: 0.8994 time to fit residues: 604.0952 Evaluate side-chains 588 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 481 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 132 VAL Chi-restraints excluded: chain b residue 139 PHE Chi-restraints excluded: chain 2 residue 13 LEU Chi-restraints excluded: chain 2 residue 127 THR Chi-restraints excluded: chain 2 residue 143 THR Chi-restraints excluded: chain 2 residue 147 THR Chi-restraints excluded: chain 6 residue 13 ILE Chi-restraints excluded: chain 6 residue 18 GLN Chi-restraints excluded: chain c residue 18 GLN Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 62 ARG Chi-restraints excluded: chain c residue 92 GLN Chi-restraints excluded: chain 7 residue 29 GLU Chi-restraints excluded: chain 7 residue 82 SER Chi-restraints excluded: chain 7 residue 162 THR Chi-restraints excluded: chain 7 residue 229 VAL Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain 5 residue 610 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 339 ARG Chi-restraints excluded: chain G residue 344 THR Chi-restraints excluded: chain G residue 440 ILE Chi-restraints excluded: chain G residue 492 VAL Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 614 THR Chi-restraints excluded: chain G residue 693 VAL Chi-restraints excluded: chain G residue 728 CYS Chi-restraints excluded: chain G residue 734 ARG Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain I residue 199 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 95 LYS Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 48 GLN Chi-restraints excluded: chain M residue 62 ARG Chi-restraints excluded: chain N residue 82 SER Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 167 THR Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 294 LEU Chi-restraints excluded: chain O residue 439 GLU Chi-restraints excluded: chain O residue 492 VAL Chi-restraints excluded: chain O residue 580 THR Chi-restraints excluded: chain O residue 614 THR Chi-restraints excluded: chain O residue 688 ARG Chi-restraints excluded: chain O residue 791 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 315 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 273 optimal weight: 0.9980 chunk 481 optimal weight: 4.9990 chunk 435 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 457 optimal weight: 4.9990 chunk 417 optimal weight: 8.9990 chunk 418 optimal weight: 4.9990 chunk 403 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 104 ASN 7 39 GLN 7 179 ASN A 92 ASN A 755 GLN C 43 GLN D 18 GLN F 39 GLN ** F 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 131 GLN G 561 GLN J 79 HIS M 92 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN O 561 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.153310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112745 restraints weight = 37578.421| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.69 r_work: 0.3047 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 40143 Z= 0.309 Angle : 0.776 9.034 54648 Z= 0.411 Chirality : 0.053 0.364 5877 Planarity : 0.006 0.063 7272 Dihedral : 6.621 59.869 5616 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.77 % Favored : 96.00 % Rotamer: Outliers : 3.42 % Allowed : 17.96 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -0.53 (0.11), residues: 5046 helix: 0.21 (0.21), residues: 567 sheet: 0.37 (0.12), residues: 1629 loop : -0.90 (0.11), residues: 2850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 219 TYR 0.031 0.003 TYR Q 195 PHE 0.022 0.003 PHE 6 111 TRP 0.021 0.003 TRP O 739 HIS 0.012 0.002 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.31 (40131) covalent geometry : angle 0.76917 / 0.41 (54612) hydrogen bonds : bond 0.05385 / 3.59 ( 1005) hydrogen bonds : angle 6.07467 / 4.20 ( 2655) metal coordination : bond 0.01855 / 1.27 ( 12) metal coordination : angle 4.09694 / 2.38 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20587.87 seconds wall clock time: 349 minutes 28.28 seconds (20968.28 seconds total)