Starting phenix.real_space_refine on Sat Aug 8 13:06:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hy0_35084/08_2026/8hy0_35084_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hy0_35084/08_2026/8hy0_35084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hy0_35084/08_2026/8hy0_35084_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hy0_35084/08_2026/8hy0_35084_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hy0_35084/08_2026/8hy0_35084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hy0_35084/08_2026/8hy0_35084.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.007 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: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 340 5.49 5 S 102 5.16 5 C 17226 2.51 5 N 5098 2.21 5 O 6048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28821 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 837 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3466 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "J" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3504 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "K" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4597 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 12, 'TRANS': 536} Chain breaks: 2 Chain: "L" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3048 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 365} Chain: "M" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2398 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Chain: "N" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3073 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 4 Chain: "O" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1275 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "P" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1249 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23908 SG CYS N 263 75.494 93.776 92.040 1.00 58.89 S ATOM 23925 SG CYS N 266 74.616 91.077 89.480 1.00 62.13 S ATOM 24078 SG CYS N 286 77.192 93.761 88.551 1.00 45.24 S ATOM 23989 SG CYS N 275 76.508 103.330 99.753 1.00 85.58 S ATOM 24010 SG CYS N 278 72.529 103.314 99.284 1.00 90.86 S ATOM 24213 SG CYS N 303 74.840 104.681 96.637 1.00 88.55 S ATOM 24236 SG CYS N 306 74.443 106.489 99.878 1.00 98.42 S ATOM 25138 SG CYS N 417 61.690 54.244 67.578 1.00 30.71 S ATOM 25165 SG CYS N 420 61.658 50.519 66.769 1.00 35.54 S ATOM 25421 SG CYS N 451 64.910 52.529 66.471 1.00 46.29 S ATOM 25326 SG CYS N 440 60.466 66.139 69.617 1.00 42.65 S ATOM 25352 SG CYS N 443 57.546 65.738 67.010 1.00 20.36 S ATOM 25541 SG CYS N 466 61.077 64.437 66.076 1.00 59.47 S ATOM 27616 SG CYS P 263 29.608 108.959 29.751 1.00101.72 S ATOM 27633 SG CYS P 266 31.112 109.275 26.277 1.00108.72 S ATOM 27786 SG CYS P 286 29.713 105.852 27.160 1.00 95.81 S ATOM 27697 SG CYS P 275 24.784 106.389 41.257 1.00141.65 S ATOM 27718 SG CYS P 278 28.049 107.182 41.453 1.00142.16 S ATOM 27921 SG CYS P 303 27.780 103.591 40.423 1.00119.98 S ATOM 27944 SG CYS P 306 26.139 104.585 43.706 1.00139.05 S Time building chain proxies: 5.06, per 1000 atoms: 0.18 Number of scatterers: 28821 At special positions: 0 Unit cell: (139.65, 158.55, 199.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 102 16.00 P 340 15.00 O 6048 8.00 N 5098 7.00 C 17226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 815.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 501 " pdb="ZN ZN L 501 " - pdb=" ND1 HIS L 188 " pdb=" ZN N 701 " pdb="ZN ZN N 701 " - pdb=" ND1 HIS N 283 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 266 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 263 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 286 " pdb=" ZN N 702 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 303 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 306 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 278 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 275 " pdb=" ZN N 703 " pdb="ZN ZN N 703 " - pdb=" ND1 HIS N 448 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 417 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 451 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 420 " pdb=" ZN N 704 " pdb="ZN ZN N 704 " - pdb=" NE2 HIS N 469 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 443 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 466 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 440 " pdb=" ZN P 701 " pdb="ZN ZN P 701 " - pdb=" ND1 HIS P 283 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 266 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 263 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 286 " pdb=" ZN P 702 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 275 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 303 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 278 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 306 " Number of angles added : 24 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 20 sheets defined 58.0% alpha, 5.8% beta 168 base pairs and 299 stacking pairs defined. Time for finding SS restraints: 5.42 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 87 through 114 removed outlier: 3.712A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.545A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.523A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.292A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.660A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 34 through 44 removed outlier: 3.504A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 88 through 99 removed outlier: 3.534A pdb=" N ALA D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.474A pdb=" N GLU D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 113 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.519A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 74 removed outlier: 4.027A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 28 through 37 removed outlier: 3.644A pdb=" N LEU G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.065A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.876A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.916A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 662 through 677 removed outlier: 5.208A pdb=" N PHE K 669 " --> pdb=" O GLU K 665 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU K 670 " --> pdb=" O VAL K 666 " (cutoff:3.500A) Processing helix chain 'K' and resid 678 through 694 Processing helix chain 'K' and resid 698 through 710 Processing helix chain 'K' and resid 715 through 725 removed outlier: 3.625A pdb=" N GLY K 725 " --> pdb=" O LYS K 721 " (cutoff:3.500A) Processing helix chain 'K' and resid 759 through 764 removed outlier: 3.740A pdb=" N PHE K 764 " --> pdb=" O LYS K 760 " (cutoff:3.500A) Processing helix chain 'K' and resid 771 through 778 Processing helix chain 'K' and resid 785 through 790 Processing helix chain 'K' and resid 801 through 840 removed outlier: 4.063A pdb=" N ASN K 840 " --> pdb=" O ASN K 836 " (cutoff:3.500A) Processing helix chain 'K' and resid 852 through 857 removed outlier: 4.311A pdb=" N GLY K 856 " --> pdb=" O PRO K 853 " (cutoff:3.500A) Processing helix chain 'K' and resid 861 through 871 Processing helix chain 'K' and resid 872 through 886 removed outlier: 4.344A pdb=" N PHE K 877 " --> pdb=" O LYS K 873 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU K 878 " --> pdb=" O GLU K 874 " (cutoff:3.500A) Processing helix chain 'K' and resid 886 through 928 removed outlier: 3.645A pdb=" N THR K 890 " --> pdb=" O HIS K 886 " (cutoff:3.500A) Proline residue: K 892 - end of helix removed outlier: 3.759A pdb=" N VAL K 915 " --> pdb=" O GLU K 911 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE K 925 " --> pdb=" O GLN K 921 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYS K 926 " --> pdb=" O LYS K 922 " (cutoff:3.500A) Processing helix chain 'K' and resid 934 through 943 Processing helix chain 'K' and resid 944 through 964 removed outlier: 3.637A pdb=" N ILE K 952 " --> pdb=" O LEU K 948 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE K 964 " --> pdb=" O THR K 960 " (cutoff:3.500A) Processing helix chain 'K' and resid 982 through 999 removed outlier: 3.889A pdb=" N TYR K 986 " --> pdb=" O LYS K 982 " (cutoff:3.500A) Processing helix chain 'K' and resid 1003 through 1022 Processing helix chain 'K' and resid 1025 through 1033 Processing helix chain 'K' and resid 1141 through 1164 removed outlier: 3.534A pdb=" N ILE K1161 " --> pdb=" O ARG K1157 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET K1164 " --> pdb=" O GLU K1160 " (cutoff:3.500A) Processing helix chain 'K' and resid 1164 through 1174 Processing helix chain 'K' and resid 1178 through 1184 Processing helix chain 'K' and resid 1202 through 1216 Processing helix chain 'K' and resid 1220 through 1233 Processing helix chain 'K' and resid 1236 through 1240 Processing helix chain 'K' and resid 1241 through 1258 Processing helix chain 'K' and resid 1262 through 1275 removed outlier: 3.572A pdb=" N MET K1266 " --> pdb=" O THR K1262 " (cutoff:3.500A) Processing helix chain 'K' and resid 1279 through 1292 removed outlier: 3.654A pdb=" N GLN K1283 " --> pdb=" O SER K1279 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 42 through 55 removed outlier: 4.250A pdb=" N ARG L 46 " --> pdb=" O PRO L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.846A pdb=" N LYS L 59 " --> pdb=" O GLY L 56 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET L 61 " --> pdb=" O TYR L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 75 removed outlier: 3.559A pdb=" N MET L 74 " --> pdb=" O THR L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 89 Processing helix chain 'L' and resid 91 through 95 removed outlier: 4.003A pdb=" N LEU L 94 " --> pdb=" O PRO L 91 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU L 95 " --> pdb=" O ASP L 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 91 through 95' Processing helix chain 'L' and resid 98 through 104 Processing helix chain 'L' and resid 115 through 136 Processing helix chain 'L' and resid 164 through 175 Processing helix chain 'L' and resid 190 through 197 Processing helix chain 'L' and resid 226 through 230 removed outlier: 3.521A pdb=" N LYS L 230 " --> pdb=" O GLY L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 263 Proline residue: L 253 - end of helix Processing helix chain 'L' and resid 272 through 276 removed outlier: 3.546A pdb=" N SER L 275 " --> pdb=" O GLY L 272 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 300 removed outlier: 4.115A pdb=" N CYS L 294 " --> pdb=" O GLY L 290 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL L 295 " --> pdb=" O HIS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 329 Processing helix chain 'L' and resid 343 through 347 removed outlier: 3.531A pdb=" N TYR L 347 " --> pdb=" O TYR L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 380 Processing helix chain 'L' and resid 381 through 383 No H-bonds generated for 'chain 'L' and resid 381 through 383' Processing helix chain 'M' and resid 85 through 89 Processing helix chain 'M' and resid 101 through 131 Processing helix chain 'M' and resid 225 through 241 Processing helix chain 'M' and resid 254 through 266 removed outlier: 3.645A pdb=" N GLU M 262 " --> pdb=" O LEU M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 297 removed outlier: 4.770A pdb=" N GLY M 294 " --> pdb=" O ASP M 290 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASN M 295 " --> pdb=" O LYS M 291 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU M 297 " --> pdb=" O LEU M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 316 removed outlier: 4.417A pdb=" N GLN M 305 " --> pdb=" O LEU M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 327 through 344 removed outlier: 3.689A pdb=" N LEU M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 339 - end of helix Processing helix chain 'M' and resid 348 through 369 removed outlier: 3.988A pdb=" N MET M 368 " --> pdb=" O VAL M 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS M 369 " --> pdb=" O TRP M 365 " (cutoff:3.500A) Processing helix chain 'M' and resid 369 through 374 Processing helix chain 'M' and resid 391 through 401 removed outlier: 4.288A pdb=" N MET M 401 " --> pdb=" O VAL M 397 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 104 Processing helix chain 'N' and resid 120 through 128 removed outlier: 4.696A pdb=" N GLU N 126 " --> pdb=" O LYS N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 175 Processing helix chain 'N' and resid 303 through 315 Processing helix chain 'N' and resid 318 through 330 Processing helix chain 'N' and resid 336 through 343 removed outlier: 3.760A pdb=" N ILE N 343 " --> pdb=" O LEU N 339 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 359 Processing helix chain 'N' and resid 382 through 387 Processing helix chain 'N' and resid 430 through 434 Processing helix chain 'N' and resid 546 through 578 removed outlier: 3.745A pdb=" N PHE N 569 " --> pdb=" O LYS N 565 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU N 571 " --> pdb=" O PHE N 567 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER N 572 " --> pdb=" O GLN N 568 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU N 577 " --> pdb=" O LEU N 573 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL N 578 " --> pdb=" O ILE N 574 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 241 removed outlier: 3.553A pdb=" N LYS O 229 " --> pdb=" O PRO O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 269 removed outlier: 4.282A pdb=" N GLN O 267 " --> pdb=" O HIS O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 271 through 293 Processing helix chain 'O' and resid 302 through 314 Processing helix chain 'O' and resid 327 through 343 removed outlier: 3.717A pdb=" N LEU O 331 " --> pdb=" O GLY O 327 " (cutoff:3.500A) Proline residue: O 339 - end of helix removed outlier: 3.615A pdb=" N SER O 343 " --> pdb=" O PRO O 339 " (cutoff:3.500A) Processing helix chain 'O' and resid 349 through 369 removed outlier: 4.011A pdb=" N HIS O 369 " --> pdb=" O TRP O 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 369 through 374 removed outlier: 4.220A pdb=" N TYR O 373 " --> pdb=" O HIS O 369 " (cutoff:3.500A) Processing helix chain 'P' and resid 303 through 313 Processing helix chain 'P' and resid 315 through 330 removed outlier: 3.713A pdb=" N LEU P 319 " --> pdb=" O SER P 315 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN P 330 " --> pdb=" O PHE P 326 " (cutoff:3.500A) Processing helix chain 'P' and resid 333 through 337 Processing helix chain 'P' and resid 338 through 345 removed outlier: 3.657A pdb=" N ASN P 342 " --> pdb=" O LYS P 338 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE P 343 " --> pdb=" O LEU P 339 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP P 344 " --> pdb=" O LEU P 340 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER P 345 " --> pdb=" O PHE P 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 338 through 345' Processing helix chain 'P' and resid 354 through 359 Processing helix chain 'P' and resid 544 through 580 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.820A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.002A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.598A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.433A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.807A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 756 through 757 Processing sheet with id=AB1, first strand: chain 'K' and resid 975 through 978 removed outlier: 3.703A pdb=" N HIS K1311 " --> pdb=" O ASP K1306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP K1306 " --> pdb=" O HIS K1311 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 233 through 238 removed outlier: 7.680A pdb=" N VAL L 234 " --> pdb=" O VAL L 203 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR L 205 " --> pdb=" O VAL L 234 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL L 236 " --> pdb=" O THR L 205 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER L 207 " --> pdb=" O VAL L 236 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU L 238 " --> pdb=" O SER L 207 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS L 209 " --> pdb=" O LEU L 238 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL L 180 " --> pdb=" O MET L 204 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N CYS L 206 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR L 182 " --> pdb=" O CYS L 206 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE L 208 " --> pdb=" O TYR L 182 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP L 184 " --> pdb=" O PHE L 208 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LYS L 210 " --> pdb=" O ASP L 184 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU L 181 " --> pdb=" O VAL L 268 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLN L 270 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE L 183 " --> pdb=" O GLN L 270 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA L 22 " --> pdb=" O VAL L 143 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL L 21 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR L 64 " --> pdb=" O VAL L 21 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR L 23 " --> pdb=" O TYR L 64 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA L 66 " --> pdb=" O TYR L 23 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE L 63 " --> pdb=" O GLU N 177 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N SER N 179 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG L 65 " --> pdb=" O SER N 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.564A pdb=" N PHE M 78 " --> pdb=" O LEU M 28 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'M' and resid 244 through 246 Processing sheet with id=AB6, first strand: chain 'N' and resid 85 through 87 removed outlier: 3.642A pdb=" N GLU N 86 " --> pdb=" O LYS N 95 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS N 95 " --> pdb=" O GLU N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'N' and resid 365 through 366 Processing sheet with id=AB8, first strand: chain 'N' and resid 437 through 439 Processing sheet with id=AB9, first strand: chain 'N' and resid 473 through 477 Processing sheet with id=AC1, first strand: chain 'N' and resid 505 through 506 removed outlier: 6.961A pdb=" N TYR N 506 " --> pdb=" O GLN P 541 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ASP P 543 " --> pdb=" O TYR N 506 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLN N 521 " --> pdb=" O ILE P 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'P' and resid 273 through 274 removed outlier: 3.825A pdb=" N PHE P 282 " --> pdb=" O LEU P 273 " (cutoff:3.500A) 1109 hydrogen bonds defined for protein. 3225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 429 hydrogen bonds 858 hydrogen bond angles 0 basepair planarities 168 basepair parallelities 299 stacking parallelities Total time for adding SS restraints: 10.49 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4859 1.32 - 1.45: 9268 1.45 - 1.57: 15130 1.57 - 1.69: 680 1.69 - 1.81: 157 Bond restraints: 30094 Sorted by residual: bond pdb=" CA ARG L 44 " pdb=" C ARG L 44 " ideal model delta sigma weight residual 1.522 1.449 0.073 1.37e-02 5.33e+03 2.83e+01 bond pdb=" CA ARG D 96 " pdb=" C ARG D 96 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.29e-02 6.01e+03 2.24e+01 bond pdb=" CA LEU A 82 " pdb=" C LEU A 82 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.26e-02 6.30e+03 2.11e+01 bond pdb=" CA LYS F 79 " pdb=" C LYS F 79 " ideal model delta sigma weight residual 1.521 1.465 0.056 1.27e-02 6.20e+03 1.93e+01 bond pdb=" CA ALA D 107 " pdb=" C ALA D 107 " ideal model delta sigma weight residual 1.523 1.487 0.037 8.40e-03 1.42e+04 1.90e+01 ... (remaining 30089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.01: 41693 4.01 - 8.03: 344 8.03 - 12.04: 25 12.04 - 16.06: 3 16.06 - 20.07: 2 Bond angle restraints: 42067 Sorted by residual: angle pdb=" C ASN N 259 " pdb=" N GLU N 260 " pdb=" CA GLU N 260 " ideal model delta sigma weight residual 122.03 101.96 20.07 2.01e+00 2.48e-01 9.97e+01 angle pdb=" N ILE B 50 " pdb=" CA ILE B 50 " pdb=" C ILE B 50 " ideal model delta sigma weight residual 112.12 104.02 8.10 8.40e-01 1.42e+00 9.30e+01 angle pdb=" N GLU A 133 " pdb=" CA GLU A 133 " pdb=" C GLU A 133 " ideal model delta sigma weight residual 113.97 101.71 12.26 1.28e+00 6.10e-01 9.18e+01 angle pdb=" O ASN N 259 " pdb=" C ASN N 259 " pdb=" N GLU N 260 " ideal model delta sigma weight residual 122.23 134.15 -11.92 1.33e+00 5.65e-01 8.04e+01 angle pdb=" CA ASN N 259 " pdb=" C ASN N 259 " pdb=" N GLU N 260 " ideal model delta sigma weight residual 115.82 102.63 13.19 1.60e+00 3.91e-01 6.80e+01 ... (remaining 42062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 15403 35.95 - 71.89: 1872 71.89 - 107.84: 22 107.84 - 143.79: 1 143.79 - 179.73: 4 Dihedral angle restraints: 17302 sinusoidal: 9403 harmonic: 7899 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual 180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA VAL K 923 " pdb=" C VAL K 923 " pdb=" N PHE K 924 " pdb=" CA PHE K 924 " ideal model delta harmonic sigma weight residual -180.00 -157.78 -22.22 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 17299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3552 0.055 - 0.111: 958 0.111 - 0.166: 122 0.166 - 0.222: 15 0.222 - 0.277: 6 Chirality restraints: 4653 Sorted by residual: chirality pdb=" CB VAL O 337 " pdb=" CA VAL O 337 " pdb=" CG1 VAL O 337 " pdb=" CG2 VAL O 337 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB VAL L 363 " pdb=" CA VAL L 363 " pdb=" CG1 VAL L 363 " pdb=" CG2 VAL L 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB THR D 112 " pdb=" CA THR D 112 " pdb=" OG1 THR D 112 " pdb=" CG2 THR D 112 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 4650 not shown) Planarity restraints: 4165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU N 507 " 0.102 5.00e-02 4.00e+02 1.49e-01 3.55e+01 pdb=" N PRO N 508 " -0.257 5.00e-02 4.00e+02 pdb=" CA PRO N 508 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO N 508 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 101 " -0.026 2.00e-02 2.50e+03 5.19e-02 2.70e+01 pdb=" C VAL A 101 " 0.090 2.00e-02 2.50e+03 pdb=" O VAL A 101 " -0.033 2.00e-02 2.50e+03 pdb=" N ALA A 102 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 72 " -0.024 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C ARG A 72 " 0.088 2.00e-02 2.50e+03 pdb=" O ARG A 72 " -0.034 2.00e-02 2.50e+03 pdb=" N GLU A 73 " -0.030 2.00e-02 2.50e+03 ... (remaining 4162 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 775 2.65 - 3.21: 25669 3.21 - 3.78: 52280 3.78 - 4.34: 68889 4.34 - 4.90: 101899 Nonbonded interactions: 249512 Sorted by model distance: nonbonded pdb=" OD1 ASP L 186 " pdb="ZN ZN L 501 " model vdw 2.090 2.230 nonbonded pdb=" OD2 ASP L 274 " pdb="ZN ZN L 501 " model vdw 2.208 2.230 nonbonded pdb=" O ASN K 663 " pdb=" OG1 THR K 667 " model vdw 2.209 3.040 nonbonded pdb=" NH2 ARG B 35 " pdb=" OH TYR B 51 " model vdw 2.220 3.120 nonbonded pdb=" O ARG K1308 " pdb=" OG1 THR K1309 " model vdw 2.260 3.040 ... (remaining 249507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 34 or resid 37 through 134)) selection = (chain 'E' and (resid 12 through 13 or resid 18 or resid 38 through 134)) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = (chain 'H' and resid 29 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 37.210 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 30119 Z= 0.563 Angle : 1.036 25.415 42091 Z= 0.734 Chirality : 0.050 0.277 4653 Planarity : 0.007 0.149 4165 Dihedral : 23.110 179.735 12190 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 16.83 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.15), residues: 2640 helix: -1.16 (0.12), residues: 1420 sheet: -0.37 (0.47), residues: 122 loop : -1.26 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 369 TYR 0.033 0.002 TYR A 99 PHE 0.039 0.002 PHE N 311 TRP 0.021 0.002 TRP K1223 HIS 0.008 0.001 HIS N 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.56 (30094) covalent geometry : angle 1.02059 / 0.73 (42067) hydrogen bonds : bond 0.15677 / 10.28 ( 1532) hydrogen bonds : angle 6.60856 / 4.68 ( 4083) metal coordination : bond 0.02699 / 1.88 ( 25) metal coordination : angle 7.46250 / 3.57 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.7157 (tttt) cc_final: 0.6952 (ttpp) REVERT: B 79 LYS cc_start: 0.7371 (mmmm) cc_final: 0.6911 (mmtp) REVERT: C 41 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7807 (mp0) REVERT: C 73 ASN cc_start: 0.8402 (t0) cc_final: 0.8047 (t0) REVERT: C 92 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7868 (mp0) REVERT: D 46 HIS cc_start: 0.6425 (m-70) cc_final: 0.5835 (m90) REVERT: D 47 PRO cc_start: 0.8473 (Cg_exo) cc_final: 0.7953 (Cg_endo) REVERT: D 81 ASN cc_start: 0.8716 (m110) cc_final: 0.8280 (m110) REVERT: E 52 ARG cc_start: 0.7455 (mtt90) cc_final: 0.7073 (mtm-85) REVERT: E 94 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7534 (mm-30) REVERT: F 27 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7037 (tp-100) REVERT: F 77 LYS cc_start: 0.8470 (mttt) cc_final: 0.8266 (mttm) REVERT: F 79 LYS cc_start: 0.7558 (mttp) cc_final: 0.7237 (mtpp) REVERT: G 36 LYS cc_start: 0.8660 (mttt) cc_final: 0.8274 (mttm) REVERT: G 38 ASN cc_start: 0.8187 (m-40) cc_final: 0.7542 (m-40) REVERT: G 84 GLN cc_start: 0.7695 (tp40) cc_final: 0.7438 (tp40) REVERT: H 65 ASP cc_start: 0.7630 (t0) cc_final: 0.7184 (t0) REVERT: H 82 LYS cc_start: 0.8243 (mttt) cc_final: 0.8032 (mmmt) REVERT: H 90 GLU cc_start: 0.7501 (mp0) cc_final: 0.6542 (mp0) REVERT: K 721 LYS cc_start: 0.7541 (ttpt) cc_final: 0.7220 (tptp) REVERT: K 885 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6579 (mm-30) REVERT: K 904 GLU cc_start: 0.7540 (tt0) cc_final: 0.7091 (tt0) REVERT: K 982 LYS cc_start: 0.7849 (mttt) cc_final: 0.7429 (mmtp) REVERT: K 990 CYS cc_start: 0.7972 (t) cc_final: 0.7436 (t) REVERT: K 1015 LYS cc_start: 0.7101 (mttt) cc_final: 0.6815 (mttm) REVERT: K 1136 PHE cc_start: 0.7997 (m-80) cc_final: 0.7686 (m-80) REVERT: K 1166 GLU cc_start: 0.7627 (pp20) cc_final: 0.7194 (pm20) REVERT: K 1205 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7370 (mttm) REVERT: K 1209 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7384 (ttp-110) REVERT: K 1244 LYS cc_start: 0.7492 (mmtt) cc_final: 0.7187 (mmtm) REVERT: K 1271 LYS cc_start: 0.7976 (mttt) cc_final: 0.7533 (mttp) REVERT: L 28 ASP cc_start: 0.8461 (m-30) cc_final: 0.8239 (m-30) REVERT: L 67 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8101 (ttpp) REVERT: L 95 GLU cc_start: 0.7384 (pm20) cc_final: 0.7107 (pm20) REVERT: L 96 MET cc_start: 0.7474 (ttp) cc_final: 0.6874 (mpp) REVERT: L 98 LYS cc_start: 0.7196 (ptmt) cc_final: 0.6955 (tppt) REVERT: L 220 GLU cc_start: 0.8029 (tp30) cc_final: 0.7769 (tp30) REVERT: L 230 LYS cc_start: 0.8661 (tttm) cc_final: 0.8371 (tttp) REVERT: L 305 MET cc_start: 0.9208 (ptp) cc_final: 0.8863 (ptm) REVERT: L 335 ASP cc_start: 0.7571 (p0) cc_final: 0.6758 (t70) REVERT: M 107 MET cc_start: 0.6546 (ppp) cc_final: 0.6119 (ppp) REVERT: M 111 LEU cc_start: 0.9052 (mt) cc_final: 0.8721 (mt) REVERT: M 275 GLN cc_start: 0.6809 (mm-40) cc_final: 0.6558 (mm110) REVERT: M 353 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6721 (mt0) REVERT: M 357 LYS cc_start: 0.7254 (tmtt) cc_final: 0.6744 (tptt) REVERT: N 121 GLU cc_start: 0.7135 (mp0) cc_final: 0.6564 (mt-10) REVERT: N 267 ASN cc_start: 0.8186 (m110) cc_final: 0.7952 (m-40) REVERT: N 305 GLU cc_start: 0.7072 (tt0) cc_final: 0.6707 (mt-10) REVERT: N 352 GLN cc_start: 0.8180 (mm110) cc_final: 0.7906 (tt0) REVERT: N 375 GLU cc_start: 0.7640 (pt0) cc_final: 0.7300 (pm20) REVERT: N 393 GLN cc_start: 0.7515 (mt0) cc_final: 0.7194 (mt0) REVERT: N 413 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7241 (mmtm) REVERT: N 511 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7943 (mtpt) REVERT: N 560 MET cc_start: 0.7365 (mmm) cc_final: 0.7142 (mmm) REVERT: O 256 MET cc_start: 0.6736 (mmm) cc_final: 0.6530 (mmm) REVERT: O 278 LEU cc_start: 0.8204 (tp) cc_final: 0.7964 (tp) REVERT: P 320 LYS cc_start: 0.8376 (mttt) cc_final: 0.7953 (mtmt) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.2200 time to fit residues: 207.8921 Evaluate side-chains 485 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 68 ASN C 112 GLN D 46 HIS D 92 GLN E 19 GLN E 68 GLN E 76 GLN E 108 ASN E 113 HIS F 25 ASN G 31 HIS G 68 ASN K 694 GLN K 937 GLN K1190 GLN L 362 ASN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 393 GLN N 502 ASN N 517 ASN O 275 GLN O 295 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.198948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.127650 restraints weight = 37795.822| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.15 r_work: 0.3094 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30119 Z= 0.166 Angle : 0.656 13.685 42091 Z= 0.367 Chirality : 0.044 0.334 4653 Planarity : 0.006 0.083 4165 Dihedral : 26.506 179.620 6658 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.29 % Allowed : 18.37 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.50 (0.16), residues: 2640 helix: 0.18 (0.13), residues: 1472 sheet: -0.88 (0.48), residues: 119 loop : -0.85 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 72 TYR 0.038 0.002 TYR H 80 PHE 0.023 0.002 PHE M 17 TRP 0.014 0.001 TRP K 719 HIS 0.008 0.001 HIS P 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (30094) covalent geometry : angle 0.65116 / 0.37 (42067) hydrogen bonds : bond 0.04906 / 3.29 ( 1532) hydrogen bonds : angle 4.24637 / 2.99 ( 4083) metal coordination : bond 0.00903 / 0.46 ( 25) metal coordination : angle 3.35010 / 1.71 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 508 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8162 (p0) cc_final: 0.7850 (p0) REVERT: A 94 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: B 31 LYS cc_start: 0.8604 (tttt) cc_final: 0.8297 (tttm) REVERT: B 67 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7786 (ttp80) REVERT: B 80 THR cc_start: 0.9130 (m) cc_final: 0.8873 (p) REVERT: C 36 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8667 (mtpt) REVERT: C 73 ASN cc_start: 0.8735 (t0) cc_final: 0.8411 (t0) REVERT: C 92 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7875 (mm-30) REVERT: C 116 LEU cc_start: 0.8812 (mm) cc_final: 0.8394 (mm) REVERT: D 46 HIS cc_start: 0.8045 (m90) cc_final: 0.7782 (m170) REVERT: D 48 ASP cc_start: 0.8402 (t0) cc_final: 0.8146 (t0) REVERT: D 54 LYS cc_start: 0.9076 (mmtt) cc_final: 0.8843 (mmtt) REVERT: D 65 ASP cc_start: 0.8976 (t0) cc_final: 0.8758 (t0) REVERT: D 81 ASN cc_start: 0.9372 (m110) cc_final: 0.9159 (m110) REVERT: E 52 ARG cc_start: 0.8264 (mtt90) cc_final: 0.7901 (mtm-85) REVERT: E 94 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8114 (mm-30) REVERT: F 25 ASN cc_start: 0.8274 (m110) cc_final: 0.8025 (m-40) REVERT: F 27 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8235 (tp-100) REVERT: F 77 LYS cc_start: 0.9164 (mttt) cc_final: 0.8768 (mmmt) REVERT: F 79 LYS cc_start: 0.8679 (mttp) cc_final: 0.8365 (mtpp) REVERT: G 36 LYS cc_start: 0.9280 (mttt) cc_final: 0.9077 (mttm) REVERT: G 38 ASN cc_start: 0.8293 (m-40) cc_final: 0.7694 (t0) REVERT: G 79 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8913 (mp) REVERT: G 92 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8105 (mm-30) REVERT: H 90 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8462 (mt-10) REVERT: K 693 SER cc_start: 0.8543 (t) cc_final: 0.8255 (m) REVERT: K 721 LYS cc_start: 0.7577 (ttpt) cc_final: 0.7166 (tptp) REVERT: K 885 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6561 (mm-30) REVERT: K 904 GLU cc_start: 0.7924 (tt0) cc_final: 0.7624 (tt0) REVERT: K 982 LYS cc_start: 0.8109 (mttt) cc_final: 0.7617 (mmtp) REVERT: K 986 TYR cc_start: 0.8323 (m-10) cc_final: 0.8123 (m-10) REVERT: K 990 CYS cc_start: 0.8546 (t) cc_final: 0.8222 (t) REVERT: K 1008 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7049 (mt-10) REVERT: K 1015 LYS cc_start: 0.7733 (mttt) cc_final: 0.7259 (mptp) REVERT: K 1155 TYR cc_start: 0.9206 (t80) cc_final: 0.8911 (t80) REVERT: K 1166 GLU cc_start: 0.8034 (pp20) cc_final: 0.7525 (pm20) REVERT: K 1182 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7553 (tppt) REVERT: K 1194 MET cc_start: 0.8395 (mtp) cc_final: 0.8081 (mtt) REVERT: K 1205 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7697 (mttm) REVERT: K 1209 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7791 (ttp-110) REVERT: K 1244 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7660 (mmtm) REVERT: K 1271 LYS cc_start: 0.7980 (mttt) cc_final: 0.7560 (mttm) REVERT: K 1310 LEU cc_start: 0.8638 (mp) cc_final: 0.8274 (mt) REVERT: L 46 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8183 (ptp-170) REVERT: L 95 GLU cc_start: 0.7831 (pm20) cc_final: 0.7594 (pm20) REVERT: L 96 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7600 (mpp) REVERT: L 335 ASP cc_start: 0.7860 (p0) cc_final: 0.7066 (t70) REVERT: M 97 ILE cc_start: 0.8390 (tt) cc_final: 0.7993 (tt) REVERT: M 247 ARG cc_start: 0.8584 (mtp180) cc_final: 0.8224 (mtp180) REVERT: M 260 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7977 (ttpp) REVERT: M 275 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6755 (mm110) REVERT: M 353 GLN cc_start: 0.7495 (mm-40) cc_final: 0.6989 (mt0) REVERT: M 357 LYS cc_start: 0.7976 (tmtt) cc_final: 0.7492 (ttpt) REVERT: N 116 ASN cc_start: 0.7771 (m-40) cc_final: 0.7524 (m-40) REVERT: N 121 GLU cc_start: 0.7399 (mp0) cc_final: 0.6830 (mt-10) REVERT: N 173 GLU cc_start: 0.7406 (tt0) cc_final: 0.7162 (tt0) REVERT: N 175 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7071 (ptp) REVERT: N 267 ASN cc_start: 0.8327 (m110) cc_final: 0.8109 (m-40) REVERT: N 292 ASP cc_start: 0.7472 (t70) cc_final: 0.7178 (t70) REVERT: N 305 GLU cc_start: 0.6990 (tt0) cc_final: 0.6478 (mt-10) REVERT: N 375 GLU cc_start: 0.8210 (pt0) cc_final: 0.7816 (pm20) REVERT: N 386 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7234 (mt) REVERT: N 393 GLN cc_start: 0.8208 (mt0) cc_final: 0.7999 (mt0) REVERT: N 413 LYS cc_start: 0.8460 (mtmt) cc_final: 0.7743 (mmtm) REVERT: N 512 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8245 (mm) REVERT: N 515 GLN cc_start: 0.8108 (mt0) cc_final: 0.7496 (mm-40) REVERT: N 560 MET cc_start: 0.7296 (mmm) cc_final: 0.6856 (mmm) REVERT: O 256 MET cc_start: 0.6586 (mmm) cc_final: 0.6275 (mmm) REVERT: O 278 LEU cc_start: 0.7336 (tp) cc_final: 0.7130 (tp) REVERT: O 296 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6633 (mpp) REVERT: P 328 LYS cc_start: 0.7557 (tptt) cc_final: 0.7016 (tptt) outliers start: 55 outliers final: 27 residues processed: 542 average time/residue: 0.1969 time to fit residues: 167.0979 Evaluate side-chains 507 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 470 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain M residue 260 LYS Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 337 VAL Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 386 LEU Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 296 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 57 optimal weight: 8.9990 chunk 173 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 18 optimal weight: 0.4980 chunk 204 optimal weight: 9.9990 chunk 134 optimal weight: 0.6980 chunk 253 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 106 HIS K 678 ASN K 694 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 562 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.199823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128300 restraints weight = 37803.696| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.15 r_work: 0.3090 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 30119 Z= 0.143 Angle : 0.586 10.625 42091 Z= 0.331 Chirality : 0.042 0.336 4653 Planarity : 0.005 0.060 4165 Dihedral : 26.508 179.185 6658 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.62 % Allowed : 18.95 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.22 (0.16), residues: 2640 helix: 0.87 (0.13), residues: 1476 sheet: -0.91 (0.46), residues: 117 loop : -0.67 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 110 TYR 0.021 0.001 TYR E 54 PHE 0.018 0.002 PHE H 67 TRP 0.010 0.001 TRP M 31 HIS 0.014 0.001 HIS P 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (30094) covalent geometry : angle 0.58166 / 0.33 (42067) hydrogen bonds : bond 0.04163 / 2.81 ( 1532) hydrogen bonds : angle 3.90169 / 2.76 ( 4083) metal coordination : bond 0.01612 / 0.81 ( 25) metal coordination : angle 3.01272 / 1.53 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 494 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8213 (mt) REVERT: A 74 ILE cc_start: 0.8729 (tp) cc_final: 0.8428 (tp) REVERT: A 81 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7638 (p0) REVERT: B 31 LYS cc_start: 0.8534 (tttt) cc_final: 0.8251 (tttm) REVERT: B 67 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7697 (ttp80) REVERT: C 36 LYS cc_start: 0.8879 (mtpt) cc_final: 0.8571 (mtpt) REVERT: C 73 ASN cc_start: 0.8751 (t0) cc_final: 0.8359 (t0) REVERT: D 46 HIS cc_start: 0.7948 (m90) cc_final: 0.7745 (m170) REVERT: D 54 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8792 (mmtt) REVERT: D 105 LYS cc_start: 0.8227 (mmmt) cc_final: 0.7836 (mmtp) REVERT: E 64 LYS cc_start: 0.8375 (mttm) cc_final: 0.8167 (mttm) REVERT: F 27 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8199 (tp-100) REVERT: F 77 LYS cc_start: 0.9135 (mttt) cc_final: 0.8761 (mmmt) REVERT: F 79 LYS cc_start: 0.8481 (mttp) cc_final: 0.8092 (mtpp) REVERT: F 80 THR cc_start: 0.8191 (t) cc_final: 0.7890 (t) REVERT: G 36 LYS cc_start: 0.9182 (mttt) cc_final: 0.8887 (mttm) REVERT: G 38 ASN cc_start: 0.8199 (m-40) cc_final: 0.7866 (m-40) REVERT: G 79 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8773 (mp) REVERT: H 76 ARG cc_start: 0.8801 (ttm-80) cc_final: 0.8420 (ttm-80) REVERT: H 82 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8844 (mmtp) REVERT: H 90 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: K 670 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: K 707 ASP cc_start: 0.7895 (t0) cc_final: 0.7376 (t0) REVERT: K 885 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6552 (tp30) REVERT: K 982 LYS cc_start: 0.8040 (mttt) cc_final: 0.7618 (mmtp) REVERT: K 990 CYS cc_start: 0.8390 (t) cc_final: 0.8042 (t) REVERT: K 1008 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6967 (mt-10) REVERT: K 1015 LYS cc_start: 0.7702 (mttt) cc_final: 0.7002 (mmtm) REVERT: K 1166 GLU cc_start: 0.7891 (pp20) cc_final: 0.7462 (pm20) REVERT: K 1194 MET cc_start: 0.8286 (mtp) cc_final: 0.8001 (mtt) REVERT: K 1205 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7628 (mttm) REVERT: K 1209 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7710 (ttp-110) REVERT: K 1244 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7526 (mmtm) REVERT: K 1271 LYS cc_start: 0.8008 (mttt) cc_final: 0.7568 (mttp) REVERT: K 1310 LEU cc_start: 0.8533 (mp) cc_final: 0.8226 (mt) REVERT: L 46 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8083 (ptp-170) REVERT: L 95 GLU cc_start: 0.7606 (pm20) cc_final: 0.7367 (pm20) REVERT: L 96 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7638 (mpp) REVERT: M 37 MET cc_start: 0.6072 (mmm) cc_final: 0.5724 (tpp) REVERT: M 260 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7871 (ttpp) REVERT: M 275 GLN cc_start: 0.6920 (mm-40) cc_final: 0.6705 (mm110) REVERT: M 280 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8145 (tp30) REVERT: M 353 GLN cc_start: 0.7396 (mm-40) cc_final: 0.6958 (mt0) REVERT: M 357 LYS cc_start: 0.7825 (tmtt) cc_final: 0.7381 (ttpt) REVERT: N 121 GLU cc_start: 0.7403 (mp0) cc_final: 0.6906 (mt-10) REVERT: N 292 ASP cc_start: 0.7443 (t70) cc_final: 0.7143 (t70) REVERT: N 305 GLU cc_start: 0.6826 (tt0) cc_final: 0.6274 (mt-10) REVERT: N 375 GLU cc_start: 0.8012 (pt0) cc_final: 0.7705 (pm20) REVERT: N 393 GLN cc_start: 0.8043 (mt0) cc_final: 0.7775 (mp10) REVERT: N 413 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7738 (mmtm) REVERT: N 512 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8215 (mm) REVERT: N 515 GLN cc_start: 0.7880 (mt0) cc_final: 0.7298 (mm-40) REVERT: N 560 MET cc_start: 0.7300 (mmm) cc_final: 0.6916 (mmm) REVERT: O 256 MET cc_start: 0.6303 (mmm) cc_final: 0.6017 (mmm) REVERT: O 296 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6973 (pmm) REVERT: P 557 LYS cc_start: 0.7013 (mmtm) cc_final: 0.6606 (mmtm) outliers start: 63 outliers final: 35 residues processed: 537 average time/residue: 0.2117 time to fit residues: 175.8898 Evaluate side-chains 509 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 463 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 710 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1160 GLU Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain M residue 260 LYS Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 25 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 284 optimal weight: 40.0000 chunk 274 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 253 optimal weight: 0.7980 chunk 295 optimal weight: 30.0000 chunk 217 optimal weight: 0.9980 chunk 205 optimal weight: 20.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN D 60 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 694 GLN L 76 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.196843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.125091 restraints weight = 37194.505| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.13 r_work: 0.3009 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 30119 Z= 0.200 Angle : 0.613 8.803 42091 Z= 0.339 Chirality : 0.044 0.317 4653 Planarity : 0.005 0.051 4165 Dihedral : 26.534 179.441 6658 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.25 % Allowed : 19.08 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.46 (0.16), residues: 2640 helix: 1.08 (0.14), residues: 1482 sheet: -0.79 (0.45), residues: 127 loop : -0.59 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 98 TYR 0.031 0.002 TYR E 54 PHE 0.036 0.002 PHE M 17 TRP 0.014 0.001 TRP K1151 HIS 0.023 0.001 HIS P 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (30094) covalent geometry : angle 0.60751 / 0.34 (42067) hydrogen bonds : bond 0.04200 / 2.85 ( 1532) hydrogen bonds : angle 3.80730 / 2.68 ( 4083) metal coordination : bond 0.03018 / 1.53 ( 25) metal coordination : angle 3.58546 / 1.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 493 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8323 (mt) REVERT: A 74 ILE cc_start: 0.8776 (tp) cc_final: 0.8513 (tp) REVERT: A 81 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7747 (p0) REVERT: B 31 LYS cc_start: 0.8539 (tttt) cc_final: 0.8287 (tttm) REVERT: B 67 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7522 (ttp80) REVERT: C 36 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8597 (mtpt) REVERT: C 73 ASN cc_start: 0.8745 (t0) cc_final: 0.8317 (t0) REVERT: C 94 ASN cc_start: 0.8747 (t0) cc_final: 0.8329 (t0) REVERT: D 39 TYR cc_start: 0.8888 (t80) cc_final: 0.8417 (t80) REVERT: D 54 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8770 (mmtt) REVERT: D 65 ASP cc_start: 0.8887 (t0) cc_final: 0.8603 (t0) REVERT: D 105 LYS cc_start: 0.8330 (mmmt) cc_final: 0.7881 (mttp) REVERT: E 50 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: E 64 LYS cc_start: 0.8376 (mttm) cc_final: 0.8138 (mttm) REVERT: F 27 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8257 (tp-100) REVERT: F 77 LYS cc_start: 0.9175 (mttt) cc_final: 0.8830 (mmmt) REVERT: F 79 LYS cc_start: 0.8567 (mttp) cc_final: 0.8197 (mmtm) REVERT: F 80 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8111 (t) REVERT: G 36 LYS cc_start: 0.9225 (mttt) cc_final: 0.8969 (mttm) REVERT: G 38 ASN cc_start: 0.8222 (m-40) cc_final: 0.7921 (m-40) REVERT: G 79 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8763 (mp) REVERT: H 60 ASN cc_start: 0.8459 (t0) cc_final: 0.8197 (t0) REVERT: H 82 LYS cc_start: 0.9067 (mmmt) cc_final: 0.8832 (mmtp) REVERT: H 90 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: K 670 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7326 (pm20) REVERT: K 707 ASP cc_start: 0.8058 (t0) cc_final: 0.7521 (t0) REVERT: K 710 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7703 (mt) REVERT: K 871 TYR cc_start: 0.8260 (m-80) cc_final: 0.8012 (m-80) REVERT: K 885 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6642 (tp30) REVERT: K 897 ARG cc_start: 0.7671 (tpp80) cc_final: 0.7452 (tpp-160) REVERT: K 928 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8958 (mp) REVERT: K 982 LYS cc_start: 0.8080 (mttt) cc_final: 0.7691 (mmtp) REVERT: K 1008 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6880 (mt-10) REVERT: K 1015 LYS cc_start: 0.7809 (mttt) cc_final: 0.7282 (mptp) REVERT: K 1166 GLU cc_start: 0.7937 (pp20) cc_final: 0.7517 (pm20) REVERT: K 1194 MET cc_start: 0.8347 (mtp) cc_final: 0.8050 (mtt) REVERT: K 1205 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7711 (mttm) REVERT: K 1209 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7719 (ttp-110) REVERT: K 1264 GLU cc_start: 0.6442 (mp0) cc_final: 0.6069 (mp0) REVERT: K 1271 LYS cc_start: 0.8017 (mttt) cc_final: 0.7593 (mttm) REVERT: K 1287 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.7125 (ttp80) REVERT: K 1310 LEU cc_start: 0.8518 (mp) cc_final: 0.8209 (mt) REVERT: L 46 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8123 (ptp-170) REVERT: L 95 GLU cc_start: 0.7646 (pm20) cc_final: 0.7311 (pm20) REVERT: L 96 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7693 (mtp) REVERT: L 205 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9097 (m) REVERT: L 363 VAL cc_start: 0.8958 (p) cc_final: 0.8660 (m) REVERT: M 37 MET cc_start: 0.6398 (mmm) cc_final: 0.6043 (tpp) REVERT: M 260 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7973 (ttpp) REVERT: M 275 GLN cc_start: 0.6944 (mm-40) cc_final: 0.6737 (mm110) REVERT: M 295 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.8049 (t0) REVERT: M 308 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7851 (mm-30) REVERT: M 353 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7012 (mt0) REVERT: M 357 LYS cc_start: 0.7944 (tmtt) cc_final: 0.7527 (ttpt) REVERT: N 121 GLU cc_start: 0.7442 (mp0) cc_final: 0.7014 (mt-10) REVERT: N 292 ASP cc_start: 0.7547 (t70) cc_final: 0.7189 (t70) REVERT: N 295 ASN cc_start: 0.8235 (t0) cc_final: 0.7446 (m110) REVERT: N 305 GLU cc_start: 0.6932 (tt0) cc_final: 0.6441 (mt-10) REVERT: N 375 GLU cc_start: 0.8072 (pt0) cc_final: 0.7738 (pm20) REVERT: N 413 LYS cc_start: 0.8435 (mtmt) cc_final: 0.7926 (mmtm) REVERT: N 469 HIS cc_start: 0.8626 (m-70) cc_final: 0.8306 (m-70) REVERT: N 500 LYS cc_start: 0.8340 (mmtp) cc_final: 0.7960 (mmmt) REVERT: N 511 LYS cc_start: 0.8298 (mtpt) cc_final: 0.7945 (mtmm) REVERT: N 512 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8401 (mm) REVERT: N 515 GLN cc_start: 0.7878 (mt0) cc_final: 0.7361 (mm-40) REVERT: N 560 MET cc_start: 0.7360 (mmm) cc_final: 0.6982 (mmm) REVERT: O 244 LYS cc_start: 0.4391 (mmmt) cc_final: 0.2951 (tmtt) REVERT: O 260 LYS cc_start: 0.7302 (ptmt) cc_final: 0.6863 (ptmt) REVERT: O 296 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6967 (pmm) REVERT: O 302 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6627 (mt-10) REVERT: O 308 GLU cc_start: 0.8565 (tp30) cc_final: 0.8320 (tp30) REVERT: O 311 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7747 (mppt) REVERT: P 557 LYS cc_start: 0.7050 (mmtm) cc_final: 0.6621 (mmtm) outliers start: 78 outliers final: 44 residues processed: 542 average time/residue: 0.2183 time to fit residues: 181.4338 Evaluate side-chains 535 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 475 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 710 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 889 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1191 LEU Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 260 LYS Chi-restraints excluded: chain M residue 267 GLN Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 337 VAL Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 474 VAL Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 247 optimal weight: 0.4980 chunk 224 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 236 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 249 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 291 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN D 60 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 84 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 690 ASN L 76 GLN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 393 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.197933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.129006 restraints weight = 37539.054| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.05 r_work: 0.3140 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 30119 Z= 0.132 Angle : 0.563 8.441 42091 Z= 0.317 Chirality : 0.041 0.316 4653 Planarity : 0.004 0.046 4165 Dihedral : 26.424 179.331 6658 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.79 % Allowed : 20.07 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.71 (0.16), residues: 2640 helix: 1.29 (0.14), residues: 1478 sheet: -0.79 (0.44), residues: 127 loop : -0.47 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 110 TYR 0.040 0.001 TYR F 88 PHE 0.033 0.001 PHE M 17 TRP 0.007 0.001 TRP K1151 HIS 0.010 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (30094) covalent geometry : angle 0.55943 / 0.32 (42067) hydrogen bonds : bond 0.03800 / 2.59 ( 1532) hydrogen bonds : angle 3.67430 / 2.58 ( 4083) metal coordination : bond 0.02113 / 1.06 ( 25) metal coordination : angle 2.80467 / 1.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 482 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8189 (mt) REVERT: A 74 ILE cc_start: 0.8839 (tp) cc_final: 0.8555 (tp) REVERT: A 81 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7793 (p0) REVERT: B 31 LYS cc_start: 0.8556 (tttt) cc_final: 0.8276 (tttm) REVERT: B 35 ARG cc_start: 0.8609 (ttm-80) cc_final: 0.8330 (ttm-80) REVERT: C 36 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8638 (mtpt) REVERT: C 73 ASN cc_start: 0.8797 (t0) cc_final: 0.8373 (t0) REVERT: C 99 ARG cc_start: 0.7937 (ptp-110) cc_final: 0.7548 (mtp85) REVERT: D 39 TYR cc_start: 0.8873 (t80) cc_final: 0.8434 (t80) REVERT: D 54 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8827 (mmtt) REVERT: D 65 ASP cc_start: 0.9001 (t0) cc_final: 0.8757 (t0) REVERT: E 64 LYS cc_start: 0.8415 (mttm) cc_final: 0.8207 (mttm) REVERT: F 77 LYS cc_start: 0.9188 (mttt) cc_final: 0.8821 (mmmt) REVERT: F 79 LYS cc_start: 0.8576 (mttp) cc_final: 0.8200 (mmtm) REVERT: F 80 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7973 (t) REVERT: F 84 MET cc_start: 0.8510 (tpp) cc_final: 0.8246 (tpp) REVERT: G 36 LYS cc_start: 0.9236 (mttt) cc_final: 0.8967 (mttm) REVERT: G 38 ASN cc_start: 0.8155 (m110) cc_final: 0.7881 (m-40) REVERT: G 79 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8772 (mp) REVERT: H 60 ASN cc_start: 0.8506 (t0) cc_final: 0.8231 (t0) REVERT: H 82 LYS cc_start: 0.9096 (mmmt) cc_final: 0.8855 (mmtp) REVERT: K 670 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: K 707 ASP cc_start: 0.8175 (t0) cc_final: 0.7624 (t0) REVERT: K 816 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: K 871 TYR cc_start: 0.8334 (m-80) cc_final: 0.8089 (m-80) REVERT: K 885 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6689 (tp30) REVERT: K 897 ARG cc_start: 0.7678 (tpp80) cc_final: 0.7469 (tpp-160) REVERT: K 923 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8471 (m) REVERT: K 982 LYS cc_start: 0.8068 (mttt) cc_final: 0.7646 (mmtp) REVERT: K 1008 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6866 (mt-10) REVERT: K 1015 LYS cc_start: 0.7753 (mttt) cc_final: 0.7248 (mptp) REVERT: K 1166 GLU cc_start: 0.7971 (pp20) cc_final: 0.7486 (pm20) REVERT: K 1194 MET cc_start: 0.8343 (mtp) cc_final: 0.8000 (mtt) REVERT: K 1205 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7709 (mttm) REVERT: K 1264 GLU cc_start: 0.6577 (mp0) cc_final: 0.6174 (mm-30) REVERT: K 1271 LYS cc_start: 0.7907 (mttt) cc_final: 0.7499 (ttmm) REVERT: K 1287 ARG cc_start: 0.7320 (ttm-80) cc_final: 0.7003 (ttp80) REVERT: L 46 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8148 (ptp-170) REVERT: L 95 GLU cc_start: 0.7690 (pm20) cc_final: 0.7358 (pm20) REVERT: L 96 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7576 (mmt) REVERT: L 256 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8276 (tttt) REVERT: M 37 MET cc_start: 0.6664 (mmm) cc_final: 0.6356 (tmm) REVERT: M 260 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7946 (ttpp) REVERT: M 275 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6641 (mm110) REVERT: M 280 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: M 295 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8128 (t0) REVERT: M 308 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7938 (mm-30) REVERT: M 353 GLN cc_start: 0.7493 (mm-40) cc_final: 0.6992 (mt0) REVERT: M 357 LYS cc_start: 0.7911 (tmtt) cc_final: 0.7504 (ttpt) REVERT: M 395 GLU cc_start: 0.8691 (tt0) cc_final: 0.8303 (tt0) REVERT: N 121 GLU cc_start: 0.7452 (mp0) cc_final: 0.6953 (mt-10) REVERT: N 292 ASP cc_start: 0.7563 (t70) cc_final: 0.7167 (t70) REVERT: N 295 ASN cc_start: 0.8219 (t0) cc_final: 0.7371 (m110) REVERT: N 305 GLU cc_start: 0.6850 (tt0) cc_final: 0.6262 (mt-10) REVERT: N 375 GLU cc_start: 0.8203 (pt0) cc_final: 0.7778 (pm20) REVERT: N 393 GLN cc_start: 0.8192 (mt0) cc_final: 0.7676 (mp10) REVERT: N 413 LYS cc_start: 0.8426 (mtmt) cc_final: 0.7870 (mmtm) REVERT: N 511 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7941 (mtmm) REVERT: N 512 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8353 (mm) REVERT: N 515 GLN cc_start: 0.7970 (mt0) cc_final: 0.7386 (mm-40) REVERT: O 260 LYS cc_start: 0.7309 (ptmt) cc_final: 0.6844 (ptmt) REVERT: O 296 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6972 (pmm) REVERT: P 554 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6997 (tttm) REVERT: P 557 LYS cc_start: 0.7078 (mmtm) cc_final: 0.6614 (mmtm) outliers start: 67 outliers final: 43 residues processed: 524 average time/residue: 0.1977 time to fit residues: 159.7177 Evaluate side-chains 521 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 463 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 76 GLN Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain M residue 94 TYR Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 260 LYS Chi-restraints excluded: chain M residue 267 GLN Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 390 THR Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 293 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 191 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 153 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.198451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128698 restraints weight = 37460.083| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.14 r_work: 0.3065 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 30119 Z= 0.130 Angle : 0.558 8.063 42091 Z= 0.313 Chirality : 0.041 0.307 4653 Planarity : 0.004 0.045 4165 Dihedral : 26.358 179.500 6658 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.17 % Allowed : 19.78 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.86 (0.16), residues: 2640 helix: 1.41 (0.14), residues: 1478 sheet: -0.85 (0.45), residues: 118 loop : -0.40 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 110 TYR 0.023 0.001 TYR F 88 PHE 0.031 0.001 PHE M 17 TRP 0.006 0.001 TRP K1151 HIS 0.009 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (30094) covalent geometry : angle 0.55464 / 0.31 (42067) hydrogen bonds : bond 0.03719 / 2.54 ( 1532) hydrogen bonds : angle 3.60755 / 2.53 ( 4083) metal coordination : bond 0.01521 / 0.76 ( 25) metal coordination : angle 2.56313 / 1.29 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 467 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.7657 (pttm) cc_final: 0.7282 (pttt) REVERT: A 61 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8219 (mt) REVERT: A 74 ILE cc_start: 0.8817 (tp) cc_final: 0.8557 (tp) REVERT: A 81 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7835 (p0) REVERT: B 31 LYS cc_start: 0.8587 (tttt) cc_final: 0.8288 (tttm) REVERT: B 35 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8293 (ttm-80) REVERT: C 36 LYS cc_start: 0.8969 (mtpt) cc_final: 0.8640 (mtpt) REVERT: C 64 GLU cc_start: 0.8173 (pt0) cc_final: 0.7904 (tt0) REVERT: C 73 ASN cc_start: 0.8814 (t0) cc_final: 0.8403 (t0) REVERT: C 99 ARG cc_start: 0.8016 (ptp-110) cc_final: 0.7573 (mtp85) REVERT: C 116 LEU cc_start: 0.8871 (mm) cc_final: 0.8669 (mm) REVERT: D 39 TYR cc_start: 0.8865 (t80) cc_final: 0.8423 (t80) REVERT: D 65 ASP cc_start: 0.9003 (t0) cc_final: 0.8742 (t0) REVERT: D 105 LYS cc_start: 0.8367 (mmmt) cc_final: 0.7895 (mmtp) REVERT: E 50 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7386 (pt0) REVERT: F 77 LYS cc_start: 0.9175 (mttt) cc_final: 0.8821 (mmmt) REVERT: F 79 LYS cc_start: 0.8564 (mttp) cc_final: 0.8212 (mmtm) REVERT: F 80 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8024 (t) REVERT: F 84 MET cc_start: 0.8527 (tpp) cc_final: 0.8220 (tpp) REVERT: G 36 LYS cc_start: 0.9226 (mttt) cc_final: 0.9004 (mttm) REVERT: G 38 ASN cc_start: 0.7991 (m110) cc_final: 0.7765 (m-40) REVERT: G 79 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8792 (mp) REVERT: H 60 ASN cc_start: 0.8627 (t0) cc_final: 0.8354 (t0) REVERT: H 82 LYS cc_start: 0.9092 (mmmt) cc_final: 0.8875 (mmtp) REVERT: K 670 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: K 707 ASP cc_start: 0.8254 (t0) cc_final: 0.7706 (t0) REVERT: K 816 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: K 885 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6754 (tp30) REVERT: K 928 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8902 (mp) REVERT: K 982 LYS cc_start: 0.8080 (mttt) cc_final: 0.7701 (mmtp) REVERT: K 1008 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6929 (mt-10) REVERT: K 1015 LYS cc_start: 0.7793 (mttt) cc_final: 0.7298 (mptp) REVERT: K 1166 GLU cc_start: 0.8036 (pp20) cc_final: 0.7529 (pm20) REVERT: K 1194 MET cc_start: 0.8331 (mtp) cc_final: 0.8005 (mtt) REVERT: K 1205 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7746 (mttm) REVERT: K 1264 GLU cc_start: 0.6591 (mp0) cc_final: 0.6173 (mm-30) REVERT: K 1271 LYS cc_start: 0.7952 (mttt) cc_final: 0.7545 (ttmm) REVERT: K 1287 ARG cc_start: 0.7389 (ttm-80) cc_final: 0.7067 (ttp80) REVERT: L 46 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8184 (ptp-170) REVERT: L 60 LYS cc_start: 0.8358 (mttm) cc_final: 0.7703 (mttp) REVERT: L 95 GLU cc_start: 0.7745 (pm20) cc_final: 0.7416 (pm20) REVERT: L 96 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7624 (mmt) REVERT: L 204 MET cc_start: 0.9100 (ttm) cc_final: 0.8899 (tpp) REVERT: L 256 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8350 (tttt) REVERT: M 37 MET cc_start: 0.6642 (mmm) cc_final: 0.6244 (tmm) REVERT: M 280 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8329 (tp30) REVERT: M 295 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8173 (t0) REVERT: M 308 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8071 (mm-30) REVERT: M 353 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7021 (mt0) REVERT: M 357 LYS cc_start: 0.7986 (tmtt) cc_final: 0.7623 (ttpt) REVERT: N 121 GLU cc_start: 0.7442 (mp0) cc_final: 0.6930 (mt-10) REVERT: N 292 ASP cc_start: 0.7578 (t70) cc_final: 0.7172 (t70) REVERT: N 295 ASN cc_start: 0.8290 (t0) cc_final: 0.7412 (m110) REVERT: N 305 GLU cc_start: 0.6975 (tt0) cc_final: 0.6374 (mt-10) REVERT: N 342 ASN cc_start: 0.7429 (m-40) cc_final: 0.6719 (t0) REVERT: N 375 GLU cc_start: 0.8273 (pt0) cc_final: 0.7857 (pm20) REVERT: N 393 GLN cc_start: 0.8234 (mt0) cc_final: 0.7773 (mp10) REVERT: N 413 LYS cc_start: 0.8491 (mtmt) cc_final: 0.7800 (mmtm) REVERT: N 511 LYS cc_start: 0.8301 (mtpt) cc_final: 0.7974 (mtmm) REVERT: N 512 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8395 (mm) REVERT: N 515 GLN cc_start: 0.7977 (mt0) cc_final: 0.7422 (mm-40) REVERT: O 260 LYS cc_start: 0.7341 (ptmt) cc_final: 0.6860 (ptmt) REVERT: O 296 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.7047 (pmm) REVERT: P 554 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7102 (tttm) outliers start: 76 outliers final: 46 residues processed: 512 average time/residue: 0.1907 time to fit residues: 150.7412 Evaluate side-chains 521 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 460 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1249 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 390 THR Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 217 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 283 optimal weight: 8.9990 chunk 105 optimal weight: 30.0000 chunk 248 optimal weight: 0.7980 chunk 225 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 chunk 96 optimal weight: 20.0000 chunk 27 optimal weight: 0.1980 chunk 55 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.197206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.129074 restraints weight = 37494.102| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.05 r_work: 0.3046 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30119 Z= 0.161 Angle : 0.572 8.841 42091 Z= 0.319 Chirality : 0.042 0.301 4653 Planarity : 0.004 0.047 4165 Dihedral : 26.372 179.531 6658 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.46 % Allowed : 19.70 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.90 (0.16), residues: 2640 helix: 1.45 (0.14), residues: 1490 sheet: -0.84 (0.45), residues: 118 loop : -0.42 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 110 TYR 0.025 0.002 TYR M 94 PHE 0.034 0.001 PHE M 17 TRP 0.010 0.001 TRP K1151 HIS 0.008 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (30094) covalent geometry : angle 0.56825 / 0.32 (42067) hydrogen bonds : bond 0.03799 / 2.59 ( 1532) hydrogen bonds : angle 3.59551 / 2.52 ( 4083) metal coordination : bond 0.01431 / 0.74 ( 25) metal coordination : angle 2.70986 / 1.39 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 471 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8278 (mt) REVERT: A 74 ILE cc_start: 0.8841 (tp) cc_final: 0.8592 (tp) REVERT: A 81 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7774 (p0) REVERT: B 31 LYS cc_start: 0.8540 (tttt) cc_final: 0.8276 (tttm) REVERT: B 92 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8679 (ttp80) REVERT: C 36 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8646 (mtpt) REVERT: C 64 GLU cc_start: 0.8166 (pt0) cc_final: 0.7914 (tt0) REVERT: C 73 ASN cc_start: 0.8821 (t0) cc_final: 0.8368 (t0) REVERT: C 99 ARG cc_start: 0.8014 (ptp-110) cc_final: 0.7623 (mtp85) REVERT: C 116 LEU cc_start: 0.8854 (mm) cc_final: 0.8609 (mm) REVERT: D 39 TYR cc_start: 0.8791 (t80) cc_final: 0.8346 (t80) REVERT: D 65 ASP cc_start: 0.8970 (t0) cc_final: 0.8646 (t0) REVERT: D 105 LYS cc_start: 0.8317 (mmmt) cc_final: 0.7803 (mmtp) REVERT: F 77 LYS cc_start: 0.9111 (mttt) cc_final: 0.8764 (mmmt) REVERT: F 79 LYS cc_start: 0.8554 (mttp) cc_final: 0.8192 (mmtm) REVERT: F 80 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7990 (t) REVERT: F 84 MET cc_start: 0.8435 (tpp) cc_final: 0.8210 (tpp) REVERT: G 36 LYS cc_start: 0.9203 (mttt) cc_final: 0.8921 (mttm) REVERT: G 38 ASN cc_start: 0.7979 (m110) cc_final: 0.7638 (m-40) REVERT: G 79 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8730 (mp) REVERT: G 84 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8697 (tp-100) REVERT: H 60 ASN cc_start: 0.8622 (t0) cc_final: 0.8353 (t0) REVERT: H 61 SER cc_start: 0.9031 (t) cc_final: 0.8525 (m) REVERT: H 82 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8785 (mmtp) REVERT: H 110 GLU cc_start: 0.8670 (tp30) cc_final: 0.8425 (tp30) REVERT: K 670 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7363 (pm20) REVERT: K 707 ASP cc_start: 0.8150 (t0) cc_final: 0.7583 (t0) REVERT: K 816 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: K 860 MET cc_start: 0.7876 (mmm) cc_final: 0.7309 (mmt) REVERT: K 885 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6691 (tp30) REVERT: K 982 LYS cc_start: 0.7962 (mttt) cc_final: 0.7516 (mmtp) REVERT: K 996 ILE cc_start: 0.8097 (mm) cc_final: 0.7742 (mt) REVERT: K 1008 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6853 (mt-10) REVERT: K 1015 LYS cc_start: 0.7718 (mttt) cc_final: 0.7185 (mptp) REVERT: K 1155 TYR cc_start: 0.9174 (t80) cc_final: 0.8961 (t80) REVERT: K 1166 GLU cc_start: 0.8003 (pp20) cc_final: 0.7520 (pm20) REVERT: K 1179 THR cc_start: 0.8104 (p) cc_final: 0.7880 (m) REVERT: K 1194 MET cc_start: 0.8281 (mtp) cc_final: 0.7932 (mtt) REVERT: K 1205 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7680 (mttm) REVERT: K 1264 GLU cc_start: 0.6521 (mp0) cc_final: 0.6113 (mm-30) REVERT: K 1266 MET cc_start: 0.8243 (mmp) cc_final: 0.7966 (tpt) REVERT: K 1271 LYS cc_start: 0.7915 (mttt) cc_final: 0.7491 (ttmm) REVERT: K 1287 ARG cc_start: 0.7267 (ttm-80) cc_final: 0.6960 (ttp80) REVERT: L 46 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8130 (ptp-170) REVERT: L 95 GLU cc_start: 0.7674 (pm20) cc_final: 0.7322 (pm20) REVERT: L 96 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7541 (mmt) REVERT: L 336 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7392 (mptt) REVERT: L 363 VAL cc_start: 0.8988 (p) cc_final: 0.8598 (m) REVERT: M 37 MET cc_start: 0.6828 (mmm) cc_final: 0.6426 (tmm) REVERT: M 275 GLN cc_start: 0.6826 (mm-40) cc_final: 0.6579 (mm110) REVERT: M 280 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8233 (tp30) REVERT: M 291 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8462 (ttmm) REVERT: M 295 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8120 (t0) REVERT: M 308 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7944 (mm-30) REVERT: M 353 GLN cc_start: 0.7512 (mm-40) cc_final: 0.6979 (mt0) REVERT: M 357 LYS cc_start: 0.7954 (tmtt) cc_final: 0.7525 (ttpt) REVERT: M 395 GLU cc_start: 0.8737 (tt0) cc_final: 0.8441 (tt0) REVERT: N 121 GLU cc_start: 0.7361 (mp0) cc_final: 0.6847 (mt-10) REVERT: N 292 ASP cc_start: 0.7555 (t70) cc_final: 0.7144 (t70) REVERT: N 295 ASN cc_start: 0.8299 (t0) cc_final: 0.7409 (m110) REVERT: N 305 GLU cc_start: 0.6927 (tt0) cc_final: 0.6305 (mt-10) REVERT: N 342 ASN cc_start: 0.7398 (m-40) cc_final: 0.6572 (t0) REVERT: N 375 GLU cc_start: 0.8200 (pt0) cc_final: 0.7772 (pm20) REVERT: N 393 GLN cc_start: 0.8138 (mt0) cc_final: 0.7678 (mp10) REVERT: N 413 LYS cc_start: 0.8430 (mtmt) cc_final: 0.7819 (mmtm) REVERT: N 511 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7938 (mtmm) REVERT: N 512 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8407 (mm) REVERT: N 515 GLN cc_start: 0.7902 (mt0) cc_final: 0.7332 (mm-40) REVERT: N 560 MET cc_start: 0.7298 (mmm) cc_final: 0.6916 (mmm) REVERT: O 244 LYS cc_start: 0.4148 (mmmt) cc_final: 0.3923 (tptp) REVERT: O 260 LYS cc_start: 0.7311 (ptmt) cc_final: 0.6820 (ptmt) REVERT: O 267 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7340 (mp10) REVERT: O 292 CYS cc_start: 0.8117 (OUTLIER) cc_final: 0.6679 (t) REVERT: O 296 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6772 (pmm) REVERT: P 554 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.7021 (tttm) outliers start: 83 outliers final: 53 residues processed: 523 average time/residue: 0.2128 time to fit residues: 170.9466 Evaluate side-chains 527 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 457 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 981 ASP Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1191 LEU Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 474 VAL Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 294 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 120 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 274 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 60 ASN E 39 HIS E 68 GLN E 93 GLN F 64 ASN F 75 HIS ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 930 HIS K1150 HIS ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 369 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.196364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.126669 restraints weight = 37089.588| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.01 r_work: 0.3078 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 30119 Z= 0.270 Angle : 0.660 11.274 42091 Z= 0.358 Chirality : 0.046 0.295 4653 Planarity : 0.005 0.051 4165 Dihedral : 26.544 179.609 6658 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.37 % Allowed : 20.37 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.66 (0.16), residues: 2640 helix: 1.23 (0.14), residues: 1502 sheet: -0.72 (0.46), residues: 116 loop : -0.54 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 110 TYR 0.025 0.002 TYR F 88 PHE 0.031 0.002 PHE M 17 TRP 0.019 0.002 TRP K1151 HIS 0.007 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.27 (30094) covalent geometry : angle 0.65441 / 0.36 (42067) hydrogen bonds : bond 0.04303 / 2.93 ( 1532) hydrogen bonds : angle 3.77258 / 2.63 ( 4083) metal coordination : bond 0.01800 / 0.98 ( 25) metal coordination : angle 3.66598 / 1.93 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 462 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.7841 (pttm) cc_final: 0.7488 (pttt) REVERT: A 61 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8332 (mt) REVERT: A 74 ILE cc_start: 0.8787 (tp) cc_final: 0.8562 (tp) REVERT: A 81 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7749 (p0) REVERT: B 31 LYS cc_start: 0.8630 (tttt) cc_final: 0.8395 (tttm) REVERT: B 67 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7662 (ttp80) REVERT: C 36 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8693 (mtpt) REVERT: C 73 ASN cc_start: 0.8762 (t0) cc_final: 0.8359 (t0) REVERT: C 99 ARG cc_start: 0.8144 (ptp-110) cc_final: 0.7881 (mtp85) REVERT: C 116 LEU cc_start: 0.8943 (mm) cc_final: 0.8690 (mm) REVERT: D 39 TYR cc_start: 0.8917 (t80) cc_final: 0.8446 (t80) REVERT: D 65 ASP cc_start: 0.8943 (t0) cc_final: 0.8643 (t0) REVERT: D 68 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: D 90 GLU cc_start: 0.7735 (tt0) cc_final: 0.7463 (tt0) REVERT: D 105 LYS cc_start: 0.8335 (mmmt) cc_final: 0.7920 (mmtp) REVERT: F 77 LYS cc_start: 0.9154 (mttt) cc_final: 0.8887 (mmmt) REVERT: F 79 LYS cc_start: 0.8639 (mttp) cc_final: 0.8384 (mmtm) REVERT: F 80 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8125 (t) REVERT: G 36 LYS cc_start: 0.9236 (mttt) cc_final: 0.8980 (mttm) REVERT: G 38 ASN cc_start: 0.7996 (m110) cc_final: 0.7776 (m-40) REVERT: G 79 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8798 (mp) REVERT: G 84 GLN cc_start: 0.9106 (tp-100) cc_final: 0.8836 (tp-100) REVERT: H 60 ASN cc_start: 0.8837 (t0) cc_final: 0.8571 (t0) REVERT: H 76 ARG cc_start: 0.9067 (ttm-80) cc_final: 0.8722 (ttp-110) REVERT: H 82 LYS cc_start: 0.9079 (mmmt) cc_final: 0.8837 (mmtp) REVERT: H 110 GLU cc_start: 0.8666 (tp30) cc_final: 0.8453 (tp30) REVERT: K 670 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: K 707 ASP cc_start: 0.8247 (t0) cc_final: 0.7737 (t0) REVERT: K 816 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: K 860 MET cc_start: 0.8093 (mmm) cc_final: 0.7555 (mmt) REVERT: K 885 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6843 (tp30) REVERT: K 928 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9007 (mp) REVERT: K 982 LYS cc_start: 0.8215 (mttt) cc_final: 0.7730 (mtpt) REVERT: K 1008 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7012 (mt-10) REVERT: K 1015 LYS cc_start: 0.7905 (mttt) cc_final: 0.7466 (mttp) REVERT: K 1166 GLU cc_start: 0.7983 (pp20) cc_final: 0.7555 (pm20) REVERT: K 1205 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7868 (mttm) REVERT: K 1264 GLU cc_start: 0.6830 (mp0) cc_final: 0.6450 (mm-30) REVERT: K 1271 LYS cc_start: 0.8111 (mttt) cc_final: 0.7733 (ttmm) REVERT: K 1285 ILE cc_start: 0.8807 (tp) cc_final: 0.8519 (tp) REVERT: K 1287 ARG cc_start: 0.7597 (ttm-80) cc_final: 0.7289 (ttp80) REVERT: L 46 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8405 (ptt180) REVERT: L 60 LYS cc_start: 0.8525 (mttm) cc_final: 0.7932 (mttp) REVERT: L 96 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7708 (mtp) REVERT: L 204 MET cc_start: 0.9050 (ttm) cc_final: 0.8762 (tpp) REVERT: L 335 ASP cc_start: 0.7763 (p0) cc_final: 0.7144 (t70) REVERT: L 336 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7395 (mttp) REVERT: L 363 VAL cc_start: 0.9072 (p) cc_final: 0.8693 (m) REVERT: M 37 MET cc_start: 0.6652 (mmm) cc_final: 0.6270 (tmm) REVERT: M 238 TYR cc_start: 0.8888 (m-10) cc_final: 0.7847 (m-10) REVERT: M 280 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8253 (tp30) REVERT: M 291 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8523 (ttmm) REVERT: M 308 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8073 (mm-30) REVERT: M 353 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7147 (mt0) REVERT: M 357 LYS cc_start: 0.8272 (tmtt) cc_final: 0.7845 (tttp) REVERT: N 121 GLU cc_start: 0.7412 (mp0) cc_final: 0.6959 (mt-10) REVERT: N 292 ASP cc_start: 0.7655 (t70) cc_final: 0.7270 (t70) REVERT: N 295 ASN cc_start: 0.8430 (t0) cc_final: 0.7617 (m110) REVERT: N 305 GLU cc_start: 0.7218 (tt0) cc_final: 0.6791 (mt-10) REVERT: N 342 ASN cc_start: 0.7620 (m-40) cc_final: 0.6807 (t0) REVERT: N 375 GLU cc_start: 0.8241 (pt0) cc_final: 0.7916 (pm20) REVERT: N 393 GLN cc_start: 0.8215 (mt0) cc_final: 0.7862 (mp10) REVERT: N 402 ASN cc_start: 0.8568 (m-40) cc_final: 0.8352 (m-40) REVERT: N 500 LYS cc_start: 0.8495 (mmtp) cc_final: 0.8037 (mmmt) REVERT: N 512 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8662 (mt) REVERT: N 515 GLN cc_start: 0.8042 (mt0) cc_final: 0.7489 (mm-40) REVERT: N 560 MET cc_start: 0.7258 (mmm) cc_final: 0.6891 (mmm) REVERT: O 228 LEU cc_start: 0.6484 (pt) cc_final: 0.6251 (mp) REVERT: O 244 LYS cc_start: 0.4052 (mmmt) cc_final: 0.3780 (tptp) REVERT: O 260 LYS cc_start: 0.7288 (ptmt) cc_final: 0.6781 (ptmt) REVERT: O 267 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: O 292 CYS cc_start: 0.8197 (OUTLIER) cc_final: 0.6785 (t) REVERT: O 296 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6866 (pmm) REVERT: P 335 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7804 (tp) REVERT: P 351 PHE cc_start: 0.6389 (t80) cc_final: 0.6145 (t80) outliers start: 81 outliers final: 56 residues processed: 514 average time/residue: 0.1983 time to fit residues: 156.1221 Evaluate side-chains 523 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 450 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 981 ASP Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 474 VAL Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain N residue 562 GLN Chi-restraints excluded: chain O residue 226 ILE Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 335 ILE Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Chi-restraints excluded: chain P residue 555 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 162 optimal weight: 0.4980 chunk 269 optimal weight: 7.9990 chunk 272 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 ASN D 46 HIS D 60 ASN E 68 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.198006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.128296 restraints weight = 37096.047| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.00 r_work: 0.3088 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30119 Z= 0.170 Angle : 0.604 11.547 42091 Z= 0.332 Chirality : 0.043 0.299 4653 Planarity : 0.004 0.049 4165 Dihedral : 26.458 179.911 6658 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.83 % Allowed : 21.07 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.82 (0.16), residues: 2640 helix: 1.39 (0.14), residues: 1496 sheet: -0.87 (0.45), residues: 118 loop : -0.46 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 35 TYR 0.021 0.002 TYR F 88 PHE 0.030 0.001 PHE M 17 TRP 0.012 0.001 TRP L 261 HIS 0.007 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (30094) covalent geometry : angle 0.60119 / 0.33 (42067) hydrogen bonds : bond 0.03851 / 2.64 ( 1532) hydrogen bonds : angle 3.67782 / 2.56 ( 4083) metal coordination : bond 0.01552 / 0.79 ( 25) metal coordination : angle 2.33293 / 1.13 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 465 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.7852 (pttm) cc_final: 0.7514 (pttt) REVERT: A 61 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8302 (mt) REVERT: A 74 ILE cc_start: 0.8762 (tp) cc_final: 0.8544 (tp) REVERT: A 81 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7678 (p0) REVERT: B 31 LYS cc_start: 0.8567 (tttt) cc_final: 0.8331 (tttm) REVERT: C 36 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8695 (mtpt) REVERT: C 64 GLU cc_start: 0.8180 (tt0) cc_final: 0.7545 (tp30) REVERT: C 73 ASN cc_start: 0.8802 (t0) cc_final: 0.8380 (t0) REVERT: C 99 ARG cc_start: 0.8174 (ptp-110) cc_final: 0.7867 (mtp85) REVERT: C 116 LEU cc_start: 0.8930 (mm) cc_final: 0.8653 (mm) REVERT: D 39 TYR cc_start: 0.8833 (t80) cc_final: 0.8389 (t80) REVERT: D 46 HIS cc_start: 0.8087 (m-70) cc_final: 0.7522 (m170) REVERT: D 65 ASP cc_start: 0.8936 (t0) cc_final: 0.8619 (t0) REVERT: D 68 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: D 90 GLU cc_start: 0.7808 (tt0) cc_final: 0.7540 (tt0) REVERT: D 105 LYS cc_start: 0.8304 (mmmt) cc_final: 0.7885 (mmtp) REVERT: F 77 LYS cc_start: 0.9140 (mttt) cc_final: 0.8827 (mmmt) REVERT: F 79 LYS cc_start: 0.8569 (mttp) cc_final: 0.8309 (mmtp) REVERT: F 80 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7971 (t) REVERT: G 36 LYS cc_start: 0.9241 (mttt) cc_final: 0.8976 (mttm) REVERT: G 38 ASN cc_start: 0.7899 (m110) cc_final: 0.7658 (m-40) REVERT: G 79 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8757 (mp) REVERT: G 84 GLN cc_start: 0.9091 (tp-100) cc_final: 0.8832 (tp-100) REVERT: H 60 ASN cc_start: 0.8747 (t0) cc_final: 0.8234 (t0) REVERT: H 61 SER cc_start: 0.9016 (t) cc_final: 0.8496 (m) REVERT: H 82 LYS cc_start: 0.9026 (mmmt) cc_final: 0.8805 (mmtp) REVERT: H 110 GLU cc_start: 0.8698 (tp30) cc_final: 0.8487 (tp30) REVERT: K 670 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: K 707 ASP cc_start: 0.8197 (t0) cc_final: 0.7671 (t0) REVERT: K 721 LYS cc_start: 0.7607 (mttt) cc_final: 0.7183 (mtpp) REVERT: K 816 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: K 860 MET cc_start: 0.7985 (mmm) cc_final: 0.7445 (mmt) REVERT: K 885 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6782 (tp30) REVERT: K 928 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8973 (mp) REVERT: K 982 LYS cc_start: 0.8050 (mttt) cc_final: 0.7604 (mmtp) REVERT: K 1008 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6940 (mt-10) REVERT: K 1015 LYS cc_start: 0.7657 (mttt) cc_final: 0.7329 (mttp) REVERT: K 1166 GLU cc_start: 0.7957 (pp20) cc_final: 0.7518 (pm20) REVERT: K 1194 MET cc_start: 0.8227 (mtp) cc_final: 0.7909 (mtt) REVERT: K 1205 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7817 (mttm) REVERT: K 1264 GLU cc_start: 0.6631 (mp0) cc_final: 0.6223 (mm-30) REVERT: K 1271 LYS cc_start: 0.8084 (mttt) cc_final: 0.7645 (ttmm) REVERT: K 1285 ILE cc_start: 0.8745 (tp) cc_final: 0.8450 (tp) REVERT: K 1287 ARG cc_start: 0.7442 (ttm-80) cc_final: 0.7144 (ttp80) REVERT: L 46 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8158 (ptp-170) REVERT: L 60 LYS cc_start: 0.8485 (mttm) cc_final: 0.7892 (mttp) REVERT: L 96 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7733 (mtp) REVERT: L 204 MET cc_start: 0.9082 (ttm) cc_final: 0.8809 (tpp) REVERT: L 335 ASP cc_start: 0.7782 (p0) cc_final: 0.7091 (t70) REVERT: L 363 VAL cc_start: 0.9036 (p) cc_final: 0.8675 (m) REVERT: M 37 MET cc_start: 0.6918 (mmm) cc_final: 0.6464 (tmm) REVERT: M 110 ARG cc_start: 0.9217 (tmm-80) cc_final: 0.8758 (ttp80) REVERT: M 238 TYR cc_start: 0.8793 (m-10) cc_final: 0.7667 (m-10) REVERT: M 280 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8230 (tp30) REVERT: M 291 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8539 (ttmm) REVERT: M 308 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8026 (mm-30) REVERT: M 353 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7060 (mt0) REVERT: M 357 LYS cc_start: 0.8098 (tmtt) cc_final: 0.7779 (tttp) REVERT: N 121 GLU cc_start: 0.7381 (mp0) cc_final: 0.6910 (mt-10) REVERT: N 292 ASP cc_start: 0.7624 (t70) cc_final: 0.7238 (t70) REVERT: N 295 ASN cc_start: 0.8391 (t0) cc_final: 0.7556 (m110) REVERT: N 305 GLU cc_start: 0.7039 (tt0) cc_final: 0.6453 (mt-10) REVERT: N 342 ASN cc_start: 0.7562 (m-40) cc_final: 0.6693 (t0) REVERT: N 375 GLU cc_start: 0.8261 (pt0) cc_final: 0.7866 (pm20) REVERT: N 393 GLN cc_start: 0.8148 (mt0) cc_final: 0.7788 (mp10) REVERT: N 402 ASN cc_start: 0.8560 (m-40) cc_final: 0.8318 (m-40) REVERT: N 500 LYS cc_start: 0.8478 (mmtp) cc_final: 0.8015 (mmmt) REVERT: N 512 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8658 (mt) REVERT: N 515 GLN cc_start: 0.8018 (mt0) cc_final: 0.7411 (mm-40) REVERT: N 560 MET cc_start: 0.7228 (mmm) cc_final: 0.6862 (mmm) REVERT: O 244 LYS cc_start: 0.3976 (mmmt) cc_final: 0.3729 (tptp) REVERT: O 260 LYS cc_start: 0.7202 (ptmt) cc_final: 0.6720 (ptmt) REVERT: O 267 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: O 292 CYS cc_start: 0.8106 (OUTLIER) cc_final: 0.6747 (t) REVERT: O 296 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6749 (pmm) REVERT: P 351 PHE cc_start: 0.6309 (t80) cc_final: 0.6088 (t80) outliers start: 68 outliers final: 45 residues processed: 508 average time/residue: 0.2089 time to fit residues: 162.6676 Evaluate side-chains 513 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 453 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1294 MET Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain N residue 562 GLN Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 100 optimal weight: 10.0000 chunk 255 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 177 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN E 68 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.200764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133835 restraints weight = 36691.702| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.80 r_work: 0.3196 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30119 Z= 0.177 Angle : 0.610 11.333 42091 Z= 0.334 Chirality : 0.043 0.294 4653 Planarity : 0.004 0.047 4165 Dihedral : 26.417 179.744 6658 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.67 % Allowed : 21.37 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.86 (0.16), residues: 2640 helix: 1.41 (0.14), residues: 1497 sheet: -0.88 (0.45), residues: 118 loop : -0.43 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.019 0.002 TYR L 313 PHE 0.028 0.001 PHE M 17 TRP 0.013 0.001 TRP K1151 HIS 0.006 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (30094) covalent geometry : angle 0.60489 / 0.33 (42067) hydrogen bonds : bond 0.03890 / 2.66 ( 1532) hydrogen bonds : angle 3.66190 / 2.55 ( 4083) metal coordination : bond 0.01597 / 0.82 ( 25) metal coordination : angle 3.22900 / 1.65 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 457 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.7873 (pttm) cc_final: 0.7534 (pttt) REVERT: A 61 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8328 (mt) REVERT: A 81 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7593 (p0) REVERT: B 31 LYS cc_start: 0.8574 (tttt) cc_final: 0.8341 (tttm) REVERT: B 67 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7560 (ttp80) REVERT: C 36 LYS cc_start: 0.9012 (mtpt) cc_final: 0.8699 (mtpt) REVERT: C 64 GLU cc_start: 0.8062 (tt0) cc_final: 0.7652 (tp30) REVERT: C 73 ASN cc_start: 0.8732 (t0) cc_final: 0.8319 (t0) REVERT: C 99 ARG cc_start: 0.8121 (ptp-110) cc_final: 0.7915 (mtp85) REVERT: C 116 LEU cc_start: 0.8910 (mm) cc_final: 0.8650 (mm) REVERT: D 39 TYR cc_start: 0.8837 (t80) cc_final: 0.8428 (t80) REVERT: D 46 HIS cc_start: 0.8085 (m-70) cc_final: 0.7863 (m-70) REVERT: D 65 ASP cc_start: 0.8841 (t0) cc_final: 0.8566 (t0) REVERT: D 68 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: D 90 GLU cc_start: 0.7715 (tt0) cc_final: 0.7459 (tt0) REVERT: D 105 LYS cc_start: 0.8345 (mmmt) cc_final: 0.7943 (mmtp) REVERT: F 77 LYS cc_start: 0.9108 (mttt) cc_final: 0.8850 (mmmt) REVERT: F 79 LYS cc_start: 0.8515 (mttp) cc_final: 0.8308 (mmtp) REVERT: F 80 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.7984 (t) REVERT: F 84 MET cc_start: 0.8396 (tpp) cc_final: 0.8063 (mmm) REVERT: F 88 TYR cc_start: 0.8417 (m-80) cc_final: 0.7969 (m-80) REVERT: G 36 LYS cc_start: 0.9215 (mttt) cc_final: 0.8968 (mttm) REVERT: G 79 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8727 (mp) REVERT: G 84 GLN cc_start: 0.9010 (tp-100) cc_final: 0.8657 (tp-100) REVERT: H 60 ASN cc_start: 0.8644 (t0) cc_final: 0.8391 (t0) REVERT: H 61 SER cc_start: 0.9009 (t) cc_final: 0.8500 (m) REVERT: H 68 GLU cc_start: 0.8359 (tp30) cc_final: 0.7719 (mt-10) REVERT: K 670 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: K 707 ASP cc_start: 0.8121 (t0) cc_final: 0.7580 (t0) REVERT: K 721 LYS cc_start: 0.7720 (mttt) cc_final: 0.7291 (mtpp) REVERT: K 816 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: K 860 MET cc_start: 0.7954 (mmm) cc_final: 0.7454 (mmt) REVERT: K 885 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6845 (tp30) REVERT: K 896 LYS cc_start: 0.7881 (ttmt) cc_final: 0.7372 (ttpp) REVERT: K 928 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8993 (mp) REVERT: K 982 LYS cc_start: 0.8086 (mttt) cc_final: 0.7708 (mmtp) REVERT: K 1008 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7054 (mt-10) REVERT: K 1015 LYS cc_start: 0.7786 (mttt) cc_final: 0.7457 (mttp) REVERT: K 1166 GLU cc_start: 0.7979 (pp20) cc_final: 0.7603 (pm20) REVERT: K 1194 MET cc_start: 0.8302 (mtp) cc_final: 0.8012 (mtt) REVERT: K 1205 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7797 (mttm) REVERT: K 1264 GLU cc_start: 0.6589 (mp0) cc_final: 0.6252 (mm-30) REVERT: K 1271 LYS cc_start: 0.8125 (mttt) cc_final: 0.7727 (ttmm) REVERT: K 1285 ILE cc_start: 0.8808 (tp) cc_final: 0.8510 (tp) REVERT: K 1287 ARG cc_start: 0.7530 (ttm-80) cc_final: 0.7245 (ttp80) REVERT: L 46 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8178 (ptp-170) REVERT: L 60 LYS cc_start: 0.8456 (mttm) cc_final: 0.7871 (mttp) REVERT: L 96 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7591 (ttm) REVERT: L 335 ASP cc_start: 0.7716 (p0) cc_final: 0.7034 (t70) REVERT: L 363 VAL cc_start: 0.9024 (p) cc_final: 0.8681 (m) REVERT: M 37 MET cc_start: 0.6855 (mmm) cc_final: 0.6435 (tmm) REVERT: M 111 LEU cc_start: 0.8361 (mt) cc_final: 0.8026 (mt) REVERT: M 238 TYR cc_start: 0.8852 (m-10) cc_final: 0.7844 (m-10) REVERT: M 280 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8188 (tp30) REVERT: M 291 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8536 (ttmm) REVERT: M 308 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7989 (mm-30) REVERT: M 353 GLN cc_start: 0.7523 (mm-40) cc_final: 0.7100 (mt0) REVERT: M 357 LYS cc_start: 0.8240 (tmtt) cc_final: 0.7903 (tttp) REVERT: N 121 GLU cc_start: 0.7483 (mp0) cc_final: 0.7055 (mt-10) REVERT: N 292 ASP cc_start: 0.7724 (t70) cc_final: 0.7409 (t70) REVERT: N 295 ASN cc_start: 0.8560 (t0) cc_final: 0.7984 (m110) REVERT: N 305 GLU cc_start: 0.7138 (tt0) cc_final: 0.6567 (mt-10) REVERT: N 342 ASN cc_start: 0.7599 (m-40) cc_final: 0.6838 (t0) REVERT: N 375 GLU cc_start: 0.8232 (pt0) cc_final: 0.7923 (pm20) REVERT: N 393 GLN cc_start: 0.8146 (mt0) cc_final: 0.7849 (mp10) REVERT: N 402 ASN cc_start: 0.8512 (m-40) cc_final: 0.8294 (m-40) REVERT: N 512 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8693 (mt) REVERT: N 515 GLN cc_start: 0.8024 (mt0) cc_final: 0.7486 (mm-40) REVERT: N 560 MET cc_start: 0.7194 (mmm) cc_final: 0.6855 (mmm) REVERT: O 244 LYS cc_start: 0.4120 (mmmt) cc_final: 0.3886 (tptp) REVERT: O 260 LYS cc_start: 0.7245 (ptmt) cc_final: 0.6750 (ptmt) REVERT: O 267 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7204 (mp10) REVERT: O 292 CYS cc_start: 0.8109 (OUTLIER) cc_final: 0.6813 (t) REVERT: O 296 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6849 (pmm) REVERT: P 351 PHE cc_start: 0.6401 (t80) cc_final: 0.6169 (t80) outliers start: 64 outliers final: 49 residues processed: 500 average time/residue: 0.2028 time to fit residues: 155.3034 Evaluate side-chains 515 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 451 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1294 MET Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 474 VAL Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain N residue 562 GLN Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 278 LEU Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 194 optimal weight: 0.5980 chunk 202 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 90 optimal weight: 50.0000 chunk 286 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 292 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 60 ASN E 68 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 678 ASN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.202048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134048 restraints weight = 37239.726| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.91 r_work: 0.3240 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 30119 Z= 0.137 Angle : 0.588 10.806 42091 Z= 0.323 Chirality : 0.041 0.296 4653 Planarity : 0.004 0.044 4165 Dihedral : 26.338 179.565 6658 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.54 % Allowed : 21.82 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.99 (0.16), residues: 2640 helix: 1.52 (0.14), residues: 1495 sheet: -0.86 (0.45), residues: 118 loop : -0.37 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K1167 TYR 0.019 0.001 TYR H 39 PHE 0.028 0.001 PHE M 17 TRP 0.011 0.001 TRP L 261 HIS 0.006 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (30094) covalent geometry : angle 0.58422 / 0.32 (42067) hydrogen bonds : bond 0.03666 / 2.51 ( 1532) hydrogen bonds : angle 3.59118 / 2.50 ( 4083) metal coordination : bond 0.01782 / 0.87 ( 25) metal coordination : angle 2.80187 / 1.44 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10162.13 seconds wall clock time: 173 minutes 35.61 seconds (10415.61 seconds total)