Starting phenix.real_space_refine on Sat May 24 20:42:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxy_35082/05_2025/8hxy_35082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxy_35082/05_2025/8hxy_35082.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hxy_35082/05_2025/8hxy_35082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxy_35082/05_2025/8hxy_35082.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxy_35082/05_2025/8hxy_35082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxy_35082/05_2025/8hxy_35082.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 5 6.06 5 P 340 5.49 5 S 84 5.16 5 C 15578 2.51 5 N 4681 2.21 5 O 5575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26263 Number of models: 1 Model: "" Number of chains: 17 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: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2769 Classifications: {'peptide': 340} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 319} Chain breaks: 3 Chain: "P" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 272 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23908 SG CYS N 263 75.494 93.776 66.840 1.00 58.89 S ATOM 23925 SG CYS N 266 74.616 91.077 64.280 1.00 62.13 S ATOM 24078 SG CYS N 286 77.192 93.761 63.351 1.00 45.24 S ATOM 23989 SG CYS N 275 76.508 103.330 74.553 1.00 85.58 S ATOM 24010 SG CYS N 278 72.529 103.314 74.084 1.00 90.86 S ATOM 24213 SG CYS N 303 74.840 104.681 71.437 1.00 88.55 S ATOM 24236 SG CYS N 306 74.443 106.489 74.678 1.00 98.42 S ATOM 25138 SG CYS N 417 61.690 54.244 42.378 1.00 30.71 S ATOM 25165 SG CYS N 420 61.658 50.519 41.569 1.00 35.54 S ATOM 25421 SG CYS N 451 64.910 52.529 41.271 1.00 46.29 S ATOM 25326 SG CYS N 440 60.466 66.139 44.417 1.00 42.65 S ATOM 25352 SG CYS N 443 57.546 65.738 41.810 1.00 20.36 S ATOM 25541 SG CYS N 466 61.077 64.437 40.876 1.00 59.47 S Time building chain proxies: 13.86, per 1000 atoms: 0.53 Number of scatterers: 26263 At special positions: 0 Unit cell: (139.65, 158.55, 174.3, 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 5 29.99 S 84 16.00 P 340 15.00 O 5575 8.00 N 4681 7.00 C 15578 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: 6.60 Conformation dependent library (CDL) restraints added in 2.4 seconds 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 " Number of angles added : 15 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4502 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 19 sheets defined 57.1% alpha, 6.5% beta 168 base pairs and 299 stacking pairs defined. Time for finding SS restraints: 10.51 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 45 removed outlier: 3.524A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (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: 3.831A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.635A 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 1189 through 1194 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 'P' and resid 544 through 563 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 971 hydrogen bonds defined for protein. 2820 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: 16.41 Time building geometry restraints manager: 7.69 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: 4385 1.32 - 1.45: 8652 1.45 - 1.57: 13637 1.57 - 1.69: 679 1.69 - 1.81: 133 Bond restraints: 27486 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 ASP N 261 " pdb=" C ASP N 261 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.31e-02 5.83e+03 1.92e+01 ... (remaining 27481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 38151 3.66 - 7.31: 368 7.31 - 10.97: 30 10.97 - 14.62: 4 14.62 - 18.28: 2 Bond angle restraints: 38555 Sorted by residual: 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=" N HIS F 75 " pdb=" CA HIS F 75 " pdb=" C HIS F 75 " ideal model delta sigma weight residual 113.97 104.30 9.67 1.28e+00 6.10e-01 5.71e+01 angle pdb=" N GLY B 48 " pdb=" CA GLY B 48 " pdb=" C GLY B 48 " ideal model delta sigma weight residual 112.51 100.95 11.56 1.53e+00 4.27e-01 5.71e+01 angle pdb=" N HIS M 18 " pdb=" CA HIS M 18 " pdb=" C HIS M 18 " ideal model delta sigma weight residual 110.80 96.06 14.74 2.13e+00 2.20e-01 4.79e+01 ... (remaining 38550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 13846 35.95 - 71.89: 1821 71.89 - 107.84: 21 107.84 - 143.79: 1 143.79 - 179.73: 4 Dihedral angle restraints: 15693 sinusoidal: 8723 harmonic: 6970 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 15690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3449 0.055 - 0.111: 689 0.111 - 0.166: 102 0.166 - 0.221: 17 0.221 - 0.277: 5 Chirality restraints: 4262 Sorted by residual: 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 chirality pdb=" CA GLU E 50 " pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CB GLU E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 4259 not shown) Planarity restraints: 3721 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 3718 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 727 2.65 - 3.21: 23206 3.21 - 3.78: 48121 3.78 - 4.34: 63316 4.34 - 4.90: 93461 Nonbonded interactions: 228831 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 228826 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: 0.820 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: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 72.970 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 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 0.079 27503 Z= 0.453 Angle : 0.943 18.278 38570 Z= 0.598 Chirality : 0.047 0.277 4262 Planarity : 0.007 0.149 3721 Dihedral : 23.635 179.735 11191 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.10 % Allowed : 15.84 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.16), residues: 2335 helix: -1.21 (0.13), residues: 1222 sheet: -0.37 (0.47), residues: 122 loop : -1.16 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K1223 HIS 0.008 0.001 HIS N 469 PHE 0.039 0.002 PHE N 311 TYR 0.033 0.002 TYR A 99 ARG 0.012 0.001 ARG N 369 Details of bonding type rmsd hydrogen bonds : bond 0.15642 ( 1394) hydrogen bonds : angle 6.63483 ( 3678) metal coordination : bond 0.00768 ( 17) metal coordination : angle 3.24015 ( 15) covalent geometry : bond 0.00679 (27486) covalent geometry : angle 0.94094 (38555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 579 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7865 (t-90) cc_final: 0.7649 (t-90) REVERT: A 54 TYR cc_start: 0.5476 (m-10) cc_final: 0.5262 (m-10) REVERT: A 90 MET cc_start: 0.6059 (tpp) cc_final: 0.5647 (tpp) REVERT: B 31 LYS cc_start: 0.5974 (tttt) cc_final: 0.5748 (tttt) REVERT: B 79 LYS cc_start: 0.5816 (mmmm) cc_final: 0.5556 (mmtm) REVERT: B 96 THR cc_start: 0.6026 (p) cc_final: 0.5805 (p) REVERT: C 41 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7108 (mp0) REVERT: C 73 ASN cc_start: 0.6950 (t0) cc_final: 0.6593 (t0) REVERT: D 65 ASP cc_start: 0.7606 (t0) cc_final: 0.6972 (t0) REVERT: D 68 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6575 (tm-30) REVERT: D 79 HIS cc_start: 0.6219 (t-90) cc_final: 0.5864 (m170) REVERT: D 81 ASN cc_start: 0.7171 (m110) cc_final: 0.6655 (m110) REVERT: D 82 LYS cc_start: 0.7468 (tppt) cc_final: 0.7189 (mtmt) REVERT: E 90 MET cc_start: 0.6376 (mmm) cc_final: 0.6171 (mmp) REVERT: F 77 LYS cc_start: 0.7419 (mttt) cc_final: 0.7003 (mmtp) REVERT: F 78 ARG cc_start: 0.7208 (mtm110) cc_final: 0.6737 (mtm-85) REVERT: F 79 LYS cc_start: 0.6333 (mttp) cc_final: 0.5989 (mtpp) REVERT: G 36 LYS cc_start: 0.7647 (mttt) cc_final: 0.7249 (mttp) REVERT: G 38 ASN cc_start: 0.6832 (m-40) cc_final: 0.6459 (m-40) REVERT: G 74 LYS cc_start: 0.6982 (ptmm) cc_final: 0.6726 (tptt) REVERT: G 104 GLN cc_start: 0.6964 (mt0) cc_final: 0.6283 (mm110) REVERT: H 83 ARG cc_start: 0.6915 (mmt90) cc_final: 0.6471 (mmp80) REVERT: H 84 SER cc_start: 0.6461 (m) cc_final: 0.6220 (t) REVERT: H 96 ARG cc_start: 0.6857 (ttp80) cc_final: 0.6447 (ttp-110) REVERT: K 714 LYS cc_start: 0.8016 (mmtp) cc_final: 0.7764 (mtmm) REVERT: K 764 PHE cc_start: 0.7104 (m-10) cc_final: 0.6761 (m-10) REVERT: K 812 GLU cc_start: 0.7776 (tp30) cc_final: 0.7399 (tp30) REVERT: K 828 ILE cc_start: 0.8109 (mt) cc_final: 0.7883 (mt) REVERT: K 958 ASP cc_start: 0.8312 (m-30) cc_final: 0.8001 (m-30) REVERT: K 1205 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7576 (mttt) REVERT: K 1227 SER cc_start: 0.8798 (t) cc_final: 0.8474 (p) REVERT: L 53 MET cc_start: 0.8718 (mmp) cc_final: 0.8122 (mmm) REVERT: L 100 GLU cc_start: 0.7964 (mp0) cc_final: 0.7629 (mt-10) REVERT: L 105 ASN cc_start: 0.7861 (t0) cc_final: 0.7358 (t0) REVERT: L 248 ARG cc_start: 0.7744 (ttt180) cc_final: 0.7399 (ttt-90) REVERT: L 288 MET cc_start: 0.8275 (ttp) cc_final: 0.8026 (ttp) REVERT: M 296 MET cc_start: 0.7996 (ppp) cc_final: 0.7752 (ptp) REVERT: N 96 LEU cc_start: 0.5446 (pt) cc_final: 0.5190 (pt) REVERT: N 107 LYS cc_start: 0.8192 (mmtp) cc_final: 0.7763 (ttpt) REVERT: N 117 LYS cc_start: 0.7578 (mmtp) cc_final: 0.7339 (mmtt) REVERT: N 187 TRP cc_start: 0.6315 (m100) cc_final: 0.6082 (m100) REVERT: N 261 ASP cc_start: 0.8197 (m-30) cc_final: 0.7979 (m-30) REVERT: N 291 ILE cc_start: 0.7919 (mm) cc_final: 0.7581 (mt) REVERT: N 375 GLU cc_start: 0.7939 (pt0) cc_final: 0.7690 (pm20) REVERT: N 521 GLN cc_start: 0.7850 (tt0) cc_final: 0.7649 (tt0) outliers start: 2 outliers final: 1 residues processed: 579 average time/residue: 0.4525 time to fit residues: 386.6779 Evaluate side-chains 376 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 260 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 107 optimal weight: 50.0000 chunk 208 optimal weight: 50.0000 chunk 80 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 76 GLN C 73 ASN C 112 GLN D 92 GLN E 19 GLN E 39 HIS E 68 GLN E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 73 ASN H 106 HIS K 961 ASN K1311 HIS ** L 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 GLN N 130 ASN N 430 HIS P 541 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.188885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137106 restraints weight = 32003.544| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.83 r_work: 0.3451 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27503 Z= 0.182 Angle : 0.590 8.238 38570 Z= 0.333 Chirality : 0.039 0.190 4262 Planarity : 0.005 0.086 3721 Dihedral : 26.945 176.587 6335 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.66 % Allowed : 17.51 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2335 helix: 0.30 (0.14), residues: 1280 sheet: -0.39 (0.48), residues: 122 loop : -0.68 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K1151 HIS 0.006 0.001 HIS K 930 PHE 0.016 0.002 PHE K 668 TYR 0.031 0.002 TYR H 80 ARG 0.006 0.001 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 1394) hydrogen bonds : angle 3.87292 ( 3678) metal coordination : bond 0.00875 ( 17) metal coordination : angle 3.50422 ( 15) covalent geometry : bond 0.00414 (27486) covalent geometry : angle 0.58650 (38555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 399 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8432 (tp) cc_final: 0.8098 (tp) REVERT: A 90 MET cc_start: 0.8540 (tpp) cc_final: 0.8072 (tpp) REVERT: A 129 ARG cc_start: 0.8425 (tpt90) cc_final: 0.7929 (tpt90) REVERT: B 31 LYS cc_start: 0.8570 (tttt) cc_final: 0.8350 (tttt) REVERT: B 35 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8166 (mmm-85) REVERT: B 93 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7481 (mp10) REVERT: C 35 ARG cc_start: 0.8044 (mtm110) cc_final: 0.7732 (mtm-85) REVERT: C 73 ASN cc_start: 0.8358 (t0) cc_final: 0.7910 (t0) REVERT: D 65 ASP cc_start: 0.8758 (t0) cc_final: 0.8515 (t0) REVERT: D 81 ASN cc_start: 0.8643 (m110) cc_final: 0.8304 (m110) REVERT: E 112 ILE cc_start: 0.9308 (mm) cc_final: 0.9098 (mt) REVERT: F 74 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: F 79 LYS cc_start: 0.8258 (mttp) cc_final: 0.7909 (mmtm) REVERT: H 54 LYS cc_start: 0.8394 (tppt) cc_final: 0.8116 (mmmt) REVERT: H 90 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: H 110 GLU cc_start: 0.8269 (tp30) cc_final: 0.7958 (tp30) REVERT: K 695 ASP cc_start: 0.7893 (m-30) cc_final: 0.7644 (t0) REVERT: K 714 LYS cc_start: 0.8033 (mmtp) cc_final: 0.7789 (mtmm) REVERT: K 764 PHE cc_start: 0.7556 (m-10) cc_final: 0.6994 (m-10) REVERT: K 812 GLU cc_start: 0.7837 (tp30) cc_final: 0.7549 (tp30) REVERT: K 903 GLU cc_start: 0.7768 (pp20) cc_final: 0.7524 (pt0) REVERT: K 957 VAL cc_start: 0.8960 (t) cc_final: 0.8631 (t) REVERT: K 958 ASP cc_start: 0.7882 (m-30) cc_final: 0.7655 (m-30) REVERT: K 1287 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7751 (ttp80) REVERT: L 53 MET cc_start: 0.8746 (mmp) cc_final: 0.8489 (mmm) REVERT: L 61 MET cc_start: 0.8162 (ptp) cc_final: 0.7902 (ptp) REVERT: L 72 GLN cc_start: 0.8266 (tt0) cc_final: 0.7872 (tt0) REVERT: L 105 ASN cc_start: 0.8593 (t0) cc_final: 0.8315 (t0) REVERT: L 248 ARG cc_start: 0.8110 (ttt180) cc_final: 0.7864 (ttt-90) REVERT: M 296 MET cc_start: 0.8011 (ppp) cc_final: 0.7388 (ppp) REVERT: M 395 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7532 (tt0) REVERT: N 107 LYS cc_start: 0.8378 (mmtp) cc_final: 0.8176 (ttpt) REVERT: N 117 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7892 (mmmt) REVERT: N 261 ASP cc_start: 0.8485 (m-30) cc_final: 0.8250 (m-30) REVERT: N 291 ILE cc_start: 0.8137 (mm) cc_final: 0.7883 (mt) REVERT: N 375 GLU cc_start: 0.8341 (pt0) cc_final: 0.8058 (pm20) REVERT: N 496 ARG cc_start: 0.8030 (mtt-85) cc_final: 0.7723 (mtp85) REVERT: N 505 TYR cc_start: 0.7860 (m-80) cc_final: 0.7536 (m-80) REVERT: N 517 ASN cc_start: 0.7126 (t0) cc_final: 0.6921 (t0) outliers start: 56 outliers final: 21 residues processed: 438 average time/residue: 0.4264 time to fit residues: 280.2552 Evaluate side-chains 365 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 341 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 857 HIS Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1179 THR Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 28 optimal weight: 7.9990 chunk 198 optimal weight: 0.0770 chunk 103 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 194 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 91 optimal weight: 60.0000 chunk 78 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 68 GLN E 93 GLN E 113 HIS G 104 GLN H 46 HIS ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.188457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.136656 restraints weight = 31743.177| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.82 r_work: 0.3448 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27503 Z= 0.147 Angle : 0.537 7.411 38570 Z= 0.306 Chirality : 0.037 0.150 4262 Planarity : 0.004 0.066 3721 Dihedral : 26.756 178.147 6332 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.14 % Allowed : 17.94 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2335 helix: 1.07 (0.15), residues: 1279 sheet: -0.40 (0.47), residues: 122 loop : -0.49 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K1151 HIS 0.005 0.001 HIS H 46 PHE 0.011 0.001 PHE E 67 TYR 0.030 0.001 TYR A 54 ARG 0.006 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 1394) hydrogen bonds : angle 3.56530 ( 3678) metal coordination : bond 0.00671 ( 17) metal coordination : angle 3.00746 ( 15) covalent geometry : bond 0.00329 (27486) covalent geometry : angle 0.53354 (38555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 362 time to evaluate : 2.370 Fit side-chains revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8446 (tp) cc_final: 0.8201 (tp) REVERT: A 87 SER cc_start: 0.8900 (m) cc_final: 0.8508 (p) REVERT: A 90 MET cc_start: 0.8360 (tpp) cc_final: 0.7756 (tpp) REVERT: A 94 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: A 129 ARG cc_start: 0.8413 (tpt90) cc_final: 0.7917 (tpt90) REVERT: B 31 LYS cc_start: 0.8531 (tttt) cc_final: 0.8218 (tttt) REVERT: B 35 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8096 (mtp-110) REVERT: B 93 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7395 (mp10) REVERT: C 73 ASN cc_start: 0.8459 (t0) cc_final: 0.7947 (t0) REVERT: F 79 LYS cc_start: 0.8106 (mttp) cc_final: 0.7827 (mmtm) REVERT: F 84 MET cc_start: 0.8106 (tpp) cc_final: 0.7821 (mmm) REVERT: G 74 LYS cc_start: 0.7708 (tppt) cc_final: 0.7198 (mmmm) REVERT: H 54 LYS cc_start: 0.8462 (tppt) cc_final: 0.8199 (mmmt) REVERT: H 117 LYS cc_start: 0.8428 (tttt) cc_final: 0.8196 (tttm) REVERT: K 668 PHE cc_start: 0.7736 (t80) cc_final: 0.7335 (t80) REVERT: K 694 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7958 (mm-40) REVERT: K 812 GLU cc_start: 0.7860 (tp30) cc_final: 0.7550 (tp30) REVERT: K 903 GLU cc_start: 0.7832 (pp20) cc_final: 0.7589 (pt0) REVERT: K 957 VAL cc_start: 0.8849 (t) cc_final: 0.8563 (t) REVERT: K 1285 ILE cc_start: 0.8889 (mm) cc_final: 0.8613 (mm) REVERT: L 53 MET cc_start: 0.8672 (mmp) cc_final: 0.8407 (mmm) REVERT: L 61 MET cc_start: 0.8166 (ptp) cc_final: 0.7878 (ptp) REVERT: L 105 ASN cc_start: 0.8584 (t0) cc_final: 0.8354 (t0) REVERT: L 248 ARG cc_start: 0.8098 (ttt180) cc_final: 0.7781 (ttt-90) REVERT: M 280 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7660 (tp30) REVERT: M 296 MET cc_start: 0.8003 (ppp) cc_final: 0.7182 (ppp) REVERT: M 310 LEU cc_start: 0.8623 (mt) cc_final: 0.8369 (mt) REVERT: M 313 SER cc_start: 0.8619 (p) cc_final: 0.8363 (p) REVERT: M 395 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: N 107 LYS cc_start: 0.8355 (mmtp) cc_final: 0.8141 (ttpt) REVERT: N 117 LYS cc_start: 0.8264 (mmtp) cc_final: 0.7910 (mmmt) REVERT: N 175 MET cc_start: 0.7753 (mtp) cc_final: 0.7524 (mtp) REVERT: N 260 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7491 (mt-10) REVERT: N 261 ASP cc_start: 0.8512 (m-30) cc_final: 0.8262 (m-30) REVERT: N 271 SER cc_start: 0.8760 (t) cc_final: 0.8515 (m) REVERT: N 291 ILE cc_start: 0.8224 (mm) cc_final: 0.7968 (mt) REVERT: N 393 GLN cc_start: 0.8254 (mt0) cc_final: 0.7557 (mp10) outliers start: 45 outliers final: 23 residues processed: 391 average time/residue: 0.4451 time to fit residues: 259.8501 Evaluate side-chains 355 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 329 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 857 HIS Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 449 LEU Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 190 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 221 optimal weight: 0.6980 chunk 143 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN D 92 GLN G 104 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN K1165 ASN ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.178916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124172 restraints weight = 31851.763| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.04 r_work: 0.3266 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27503 Z= 0.232 Angle : 0.600 9.146 38570 Z= 0.337 Chirality : 0.040 0.195 4262 Planarity : 0.005 0.058 3721 Dihedral : 27.005 177.172 6332 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.95 % Allowed : 17.70 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2335 helix: 1.00 (0.14), residues: 1293 sheet: -0.46 (0.50), residues: 107 loop : -0.46 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K1151 HIS 0.005 0.001 HIS L 38 PHE 0.020 0.002 PHE H 67 TYR 0.036 0.002 TYR A 54 ARG 0.005 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 1394) hydrogen bonds : angle 3.65129 ( 3678) metal coordination : bond 0.01477 ( 17) metal coordination : angle 3.46043 ( 15) covalent geometry : bond 0.00539 (27486) covalent geometry : angle 0.59652 (38555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 347 time to evaluate : 2.367 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8285 (tpp) cc_final: 0.7519 (tpp) REVERT: A 94 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: B 31 LYS cc_start: 0.8538 (tttt) cc_final: 0.8141 (tttt) REVERT: B 35 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.8139 (mtp-110) REVERT: B 91 LYS cc_start: 0.8507 (tttp) cc_final: 0.8097 (mtpp) REVERT: B 93 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7525 (mm110) REVERT: C 73 ASN cc_start: 0.8303 (t0) cc_final: 0.7796 (t0) REVERT: D 31 LYS cc_start: 0.8368 (mttt) cc_final: 0.8044 (pttt) REVERT: D 65 ASP cc_start: 0.8929 (t0) cc_final: 0.8424 (t0) REVERT: E 50 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7225 (pt0) REVERT: F 79 LYS cc_start: 0.8364 (mttp) cc_final: 0.7969 (mmtm) REVERT: F 84 MET cc_start: 0.8284 (tpp) cc_final: 0.7934 (mmm) REVERT: G 74 LYS cc_start: 0.7796 (tppt) cc_final: 0.7433 (mmmm) REVERT: H 54 LYS cc_start: 0.8662 (tppt) cc_final: 0.8454 (mmmt) REVERT: H 90 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: K 719 TRP cc_start: 0.8558 (t-100) cc_final: 0.7883 (t60) REVERT: K 860 MET cc_start: 0.8534 (tpp) cc_final: 0.8313 (mmm) REVERT: K 957 VAL cc_start: 0.8845 (t) cc_final: 0.8597 (t) REVERT: K 1208 LEU cc_start: 0.6597 (mt) cc_final: 0.5819 (mp) REVERT: L 53 MET cc_start: 0.8935 (mmp) cc_final: 0.8720 (mmm) REVERT: L 61 MET cc_start: 0.8250 (ptp) cc_final: 0.7918 (ptp) REVERT: L 105 ASN cc_start: 0.8678 (t0) cc_final: 0.8438 (t0) REVERT: M 242 ASP cc_start: 0.8349 (m-30) cc_final: 0.7942 (m-30) REVERT: M 280 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: M 310 LEU cc_start: 0.8438 (mt) cc_final: 0.8139 (mt) REVERT: M 313 SER cc_start: 0.8781 (p) cc_final: 0.8568 (p) REVERT: M 395 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: N 107 LYS cc_start: 0.8562 (mmtp) cc_final: 0.8051 (ttpt) REVERT: N 260 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7648 (mt-10) REVERT: N 271 SER cc_start: 0.8828 (t) cc_final: 0.8566 (m) REVERT: N 331 ASN cc_start: 0.6389 (t0) cc_final: 0.6044 (t0) REVERT: N 346 HIS cc_start: 0.6917 (m170) cc_final: 0.6683 (m-70) REVERT: N 393 GLN cc_start: 0.8244 (mt0) cc_final: 0.7454 (mp10) REVERT: P 538 LYS cc_start: 0.8543 (ptpt) cc_final: 0.8286 (pttt) outliers start: 62 outliers final: 39 residues processed: 386 average time/residue: 0.4313 time to fit residues: 251.1279 Evaluate side-chains 361 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 317 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR 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 92 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain K residue 1295 SER Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 350 ASP Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 365 THR Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 449 LEU Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 558 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 205 optimal weight: 50.0000 chunk 145 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1165 ASN ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 GLN P 535 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.179102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124358 restraints weight = 31799.946| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.11 r_work: 0.3278 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27503 Z= 0.199 Angle : 0.570 10.595 38570 Z= 0.322 Chirality : 0.039 0.217 4262 Planarity : 0.004 0.052 3721 Dihedral : 26.855 178.033 6332 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.28 % Allowed : 17.89 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2335 helix: 1.10 (0.15), residues: 1295 sheet: -0.56 (0.50), residues: 108 loop : -0.46 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K1151 HIS 0.004 0.001 HIS K 930 PHE 0.019 0.002 PHE K1305 TYR 0.027 0.002 TYR A 54 ARG 0.006 0.000 ARG M 324 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 1394) hydrogen bonds : angle 3.57593 ( 3678) metal coordination : bond 0.01142 ( 17) metal coordination : angle 3.26471 ( 15) covalent geometry : bond 0.00461 (27486) covalent geometry : angle 0.56608 (38555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 337 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8276 (tpp) cc_final: 0.7514 (tpp) REVERT: A 94 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: A 129 ARG cc_start: 0.8529 (tpt90) cc_final: 0.8253 (tpt90) REVERT: B 31 LYS cc_start: 0.8508 (tttt) cc_final: 0.8090 (tttt) REVERT: B 35 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8087 (mtp-110) REVERT: B 91 LYS cc_start: 0.8562 (tttp) cc_final: 0.8159 (mtpp) REVERT: B 93 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7485 (mm110) REVERT: C 73 ASN cc_start: 0.8309 (t0) cc_final: 0.7785 (t0) REVERT: D 31 LYS cc_start: 0.8409 (mttt) cc_final: 0.8054 (pttt) REVERT: D 59 MET cc_start: 0.9028 (mmm) cc_final: 0.8626 (mmt) REVERT: D 65 ASP cc_start: 0.8905 (t0) cc_final: 0.8337 (t0) REVERT: E 42 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7739 (mtt-85) REVERT: E 50 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7158 (pt0) REVERT: F 79 LYS cc_start: 0.8341 (mttp) cc_final: 0.7934 (mmtm) REVERT: F 84 MET cc_start: 0.8278 (tpp) cc_final: 0.7953 (mmm) REVERT: G 74 LYS cc_start: 0.7840 (tppt) cc_final: 0.7423 (mmmm) REVERT: H 54 LYS cc_start: 0.8673 (tppt) cc_final: 0.8438 (mmmt) REVERT: H 90 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8167 (mt-10) REVERT: K 727 GLN cc_start: 0.6905 (mm-40) cc_final: 0.6624 (mp10) REVERT: K 763 THR cc_start: 0.7796 (m) cc_final: 0.7383 (p) REVERT: K 860 MET cc_start: 0.8505 (tpp) cc_final: 0.8241 (mmm) REVERT: K 957 VAL cc_start: 0.8834 (t) cc_final: 0.8590 (t) REVERT: K 1208 LEU cc_start: 0.6455 (mt) cc_final: 0.5846 (mp) REVERT: K 1268 LEU cc_start: 0.8718 (mt) cc_final: 0.8408 (mt) REVERT: L 53 MET cc_start: 0.8948 (mmp) cc_final: 0.8689 (mmm) REVERT: L 61 MET cc_start: 0.8237 (ptp) cc_final: 0.7896 (ptp) REVERT: L 105 ASN cc_start: 0.8658 (t0) cc_final: 0.8401 (t0) REVERT: L 316 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7444 (ptt-90) REVERT: L 336 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7795 (mmtm) REVERT: L 352 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8437 (mttp) REVERT: M 242 ASP cc_start: 0.8344 (m-30) cc_final: 0.7963 (m-30) REVERT: M 280 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7816 (tp30) REVERT: M 310 LEU cc_start: 0.8457 (mt) cc_final: 0.8139 (mt) REVERT: M 313 SER cc_start: 0.8789 (p) cc_final: 0.8566 (p) REVERT: M 395 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: N 107 LYS cc_start: 0.8547 (mmtp) cc_final: 0.8009 (ttpt) REVERT: N 260 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7657 (mt-10) REVERT: N 271 SER cc_start: 0.8874 (t) cc_final: 0.8607 (m) REVERT: N 331 ASN cc_start: 0.6492 (t0) cc_final: 0.6190 (t0) REVERT: N 393 GLN cc_start: 0.8191 (mt0) cc_final: 0.7427 (mp10) REVERT: P 538 LYS cc_start: 0.8553 (ptpt) cc_final: 0.8317 (pttt) outliers start: 69 outliers final: 47 residues processed: 384 average time/residue: 0.4304 time to fit residues: 247.4776 Evaluate side-chains 370 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 315 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 35 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 9 LYS 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 92 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 858 THR Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 316 ARG Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 350 ASP Chi-restraints excluded: chain L residue 352 LYS Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 449 LEU Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 555 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 203 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 chunk 217 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 249 optimal weight: 0.4980 chunk 197 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 ASN G 104 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1165 ASN ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.177896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123549 restraints weight = 31720.618| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.07 r_work: 0.3254 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27503 Z= 0.215 Angle : 0.588 10.066 38570 Z= 0.330 Chirality : 0.040 0.219 4262 Planarity : 0.005 0.052 3721 Dihedral : 26.891 177.945 6332 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.19 % Allowed : 17.94 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.17), residues: 2335 helix: 1.09 (0.14), residues: 1300 sheet: -0.51 (0.50), residues: 105 loop : -0.47 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K1151 HIS 0.006 0.001 HIS L 38 PHE 0.020 0.002 PHE K1305 TYR 0.027 0.002 TYR A 54 ARG 0.010 0.001 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 1394) hydrogen bonds : angle 3.57970 ( 3678) metal coordination : bond 0.01354 ( 17) metal coordination : angle 3.33223 ( 15) covalent geometry : bond 0.00502 (27486) covalent geometry : angle 0.58429 (38555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 323 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8238 (tpp) cc_final: 0.7495 (tpp) REVERT: A 94 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: A 129 ARG cc_start: 0.8485 (tpt90) cc_final: 0.8218 (tpt90) REVERT: B 91 LYS cc_start: 0.8541 (tttp) cc_final: 0.8057 (tttm) REVERT: B 93 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7496 (mm110) REVERT: C 73 ASN cc_start: 0.8273 (t0) cc_final: 0.7754 (t0) REVERT: D 31 LYS cc_start: 0.8417 (mttt) cc_final: 0.8055 (pttt) REVERT: D 59 MET cc_start: 0.9019 (mmm) cc_final: 0.8607 (mmt) REVERT: D 65 ASP cc_start: 0.8906 (t0) cc_final: 0.8342 (t0) REVERT: D 81 ASN cc_start: 0.8839 (m-40) cc_final: 0.8392 (m110) REVERT: E 41 TYR cc_start: 0.8766 (m-80) cc_final: 0.8278 (m-80) REVERT: E 42 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7800 (mtt-85) REVERT: E 50 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7173 (pt0) REVERT: F 79 LYS cc_start: 0.8308 (mttp) cc_final: 0.7879 (mmtm) REVERT: F 84 MET cc_start: 0.8298 (tpp) cc_final: 0.7965 (mmm) REVERT: G 74 LYS cc_start: 0.7864 (tppt) cc_final: 0.7483 (mmmm) REVERT: H 54 LYS cc_start: 0.8661 (tppt) cc_final: 0.8436 (mmmt) REVERT: H 73 GLU cc_start: 0.8979 (tp30) cc_final: 0.8778 (tp30) REVERT: H 90 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: K 727 GLN cc_start: 0.6955 (mm-40) cc_final: 0.6669 (mp10) REVERT: K 763 THR cc_start: 0.7834 (m) cc_final: 0.7430 (p) REVERT: K 860 MET cc_start: 0.8472 (tpp) cc_final: 0.8195 (mmm) REVERT: K 877 PHE cc_start: 0.7435 (m-10) cc_final: 0.7189 (m-80) REVERT: K 957 VAL cc_start: 0.8845 (t) cc_final: 0.8598 (t) REVERT: K 1129 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6447 (mm) REVERT: K 1268 LEU cc_start: 0.8739 (mt) cc_final: 0.8402 (mt) REVERT: L 61 MET cc_start: 0.8231 (ptp) cc_final: 0.7880 (ptp) REVERT: L 88 ARG cc_start: 0.8499 (mtp-110) cc_final: 0.8203 (mtp180) REVERT: L 105 ASN cc_start: 0.8664 (t0) cc_final: 0.8406 (t0) REVERT: L 336 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7793 (mtpt) REVERT: M 242 ASP cc_start: 0.8319 (m-30) cc_final: 0.7960 (m-30) REVERT: M 280 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7825 (tp30) REVERT: M 310 LEU cc_start: 0.8444 (mt) cc_final: 0.8139 (mt) REVERT: M 313 SER cc_start: 0.8764 (p) cc_final: 0.8550 (p) REVERT: M 395 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: N 107 LYS cc_start: 0.8493 (mmtp) cc_final: 0.8027 (ttpt) REVERT: N 260 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7674 (mt-10) REVERT: N 271 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8551 (m) REVERT: N 331 ASN cc_start: 0.6777 (t0) cc_final: 0.6475 (t0) REVERT: N 393 GLN cc_start: 0.8237 (mt0) cc_final: 0.7459 (mp10) REVERT: N 515 GLN cc_start: 0.8609 (mt0) cc_final: 0.7640 (pp30) REVERT: P 537 PHE cc_start: 0.8456 (m-10) cc_final: 0.8202 (m-10) REVERT: P 538 LYS cc_start: 0.8564 (ptpt) cc_final: 0.8328 (pttt) outliers start: 67 outliers final: 49 residues processed: 366 average time/residue: 0.4459 time to fit residues: 243.9046 Evaluate side-chains 364 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 307 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR 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 95 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 9 LYS 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 92 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 858 THR Chi-restraints excluded: chain K residue 903 GLU Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1129 ILE Chi-restraints excluded: chain K residue 1165 ASN Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 350 ASP Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 315 LYS Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 368 MET Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 271 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 449 LEU Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 555 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 169 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 221 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 ASN G 104 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.181251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127606 restraints weight = 31835.945| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.08 r_work: 0.3309 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27503 Z= 0.142 Angle : 0.534 11.365 38570 Z= 0.304 Chirality : 0.037 0.204 4262 Planarity : 0.004 0.052 3721 Dihedral : 26.628 178.869 6332 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.66 % Allowed : 18.60 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2335 helix: 1.40 (0.15), residues: 1301 sheet: -0.46 (0.51), residues: 106 loop : -0.37 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1151 HIS 0.003 0.001 HIS K 785 PHE 0.021 0.001 PHE K1305 TYR 0.017 0.001 TYR L 313 ARG 0.008 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 1394) hydrogen bonds : angle 3.42915 ( 3678) metal coordination : bond 0.00748 ( 17) metal coordination : angle 2.85439 ( 15) covalent geometry : bond 0.00317 (27486) covalent geometry : angle 0.53084 (38555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 325 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8811 (m) cc_final: 0.8362 (p) REVERT: A 90 MET cc_start: 0.8262 (tpp) cc_final: 0.7489 (tpp) REVERT: A 94 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: B 35 ARG cc_start: 0.8300 (ttm110) cc_final: 0.7892 (mtp-110) REVERT: B 91 LYS cc_start: 0.8521 (tttp) cc_final: 0.8024 (tttm) REVERT: B 93 GLN cc_start: 0.7554 (mm-40) cc_final: 0.7285 (mm110) REVERT: C 36 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8468 (mtmt) REVERT: C 73 ASN cc_start: 0.8281 (t0) cc_final: 0.7755 (t0) REVERT: D 31 LYS cc_start: 0.8401 (mttt) cc_final: 0.8039 (pttt) REVERT: D 65 ASP cc_start: 0.8811 (t0) cc_final: 0.8427 (t0) REVERT: E 41 TYR cc_start: 0.8734 (m-80) cc_final: 0.8174 (m-80) REVERT: E 42 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7802 (mtt-85) REVERT: E 50 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7013 (pt0) REVERT: F 79 LYS cc_start: 0.8162 (mttp) cc_final: 0.7754 (mmtm) REVERT: F 84 MET cc_start: 0.8130 (tpp) cc_final: 0.7818 (mmm) REVERT: G 74 LYS cc_start: 0.7802 (tppt) cc_final: 0.7387 (mmmm) REVERT: G 95 LYS cc_start: 0.8475 (ttmm) cc_final: 0.8179 (tttm) REVERT: H 54 LYS cc_start: 0.8590 (tppt) cc_final: 0.8387 (mmmt) REVERT: H 90 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: K 727 GLN cc_start: 0.6852 (mm-40) cc_final: 0.6607 (mp10) REVERT: K 764 PHE cc_start: 0.7708 (m-10) cc_final: 0.7223 (m-10) REVERT: K 860 MET cc_start: 0.8476 (tpp) cc_final: 0.8156 (mmm) REVERT: K 957 VAL cc_start: 0.8804 (t) cc_final: 0.8556 (t) REVERT: L 61 MET cc_start: 0.8124 (ptp) cc_final: 0.7780 (ptp) REVERT: L 105 ASN cc_start: 0.8621 (t0) cc_final: 0.8412 (t0) REVERT: L 288 MET cc_start: 0.8451 (ttp) cc_final: 0.8241 (ttp) REVERT: L 335 ASP cc_start: 0.7822 (p0) cc_final: 0.7333 (p0) REVERT: L 336 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7546 (mttt) REVERT: L 352 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8406 (mttp) REVERT: M 242 ASP cc_start: 0.8341 (m-30) cc_final: 0.7974 (m-30) REVERT: M 280 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7818 (tp30) REVERT: M 310 LEU cc_start: 0.8478 (mt) cc_final: 0.8185 (mt) REVERT: M 313 SER cc_start: 0.8745 (p) cc_final: 0.8524 (p) REVERT: M 395 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: N 107 LYS cc_start: 0.8366 (mmtp) cc_final: 0.7933 (ttpt) REVERT: N 271 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8551 (m) REVERT: N 331 ASN cc_start: 0.6529 (t0) cc_final: 0.6207 (t0) REVERT: N 393 GLN cc_start: 0.8131 (mt0) cc_final: 0.7476 (mp10) REVERT: N 515 GLN cc_start: 0.8513 (mt0) cc_final: 0.7732 (pp30) REVERT: P 537 PHE cc_start: 0.8365 (m-10) cc_final: 0.8141 (m-10) REVERT: P 538 LYS cc_start: 0.8550 (ptpt) cc_final: 0.8268 (pttt) outliers start: 56 outliers final: 38 residues processed: 360 average time/residue: 0.4390 time to fit residues: 236.2120 Evaluate side-chains 355 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 309 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 35 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 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 92 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 857 HIS Chi-restraints excluded: chain K residue 858 THR Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 352 LYS Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 368 MET Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 271 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 555 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 112 optimal weight: 0.7980 chunk 30 optimal weight: 0.0970 chunk 173 optimal weight: 0.0030 chunk 254 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 229 optimal weight: 0.0980 chunk 213 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN F 64 ASN G 31 HIS G 68 ASN K1150 HIS L 76 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.188550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.137082 restraints weight = 32106.045| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.81 r_work: 0.3460 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27503 Z= 0.124 Angle : 0.518 10.763 38570 Z= 0.295 Chirality : 0.036 0.207 4262 Planarity : 0.004 0.053 3721 Dihedral : 26.396 178.873 6332 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.09 % Allowed : 19.93 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.18), residues: 2335 helix: 1.65 (0.15), residues: 1301 sheet: -0.40 (0.50), residues: 108 loop : -0.24 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 782 HIS 0.003 0.001 HIS L 78 PHE 0.019 0.001 PHE H 67 TYR 0.013 0.001 TYR M 373 ARG 0.008 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 1394) hydrogen bonds : angle 3.30698 ( 3678) metal coordination : bond 0.00631 ( 17) metal coordination : angle 2.71195 ( 15) covalent geometry : bond 0.00266 (27486) covalent geometry : angle 0.51499 (38555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 334 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8690 (m) cc_final: 0.8421 (p) REVERT: A 90 MET cc_start: 0.8299 (tpp) cc_final: 0.7565 (mmt) REVERT: A 94 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: B 91 LYS cc_start: 0.8655 (tttp) cc_final: 0.8236 (mtpp) REVERT: C 73 ASN cc_start: 0.8451 (t0) cc_final: 0.7937 (t0) REVERT: D 31 LYS cc_start: 0.8394 (mttt) cc_final: 0.8108 (pttt) REVERT: D 65 ASP cc_start: 0.8593 (t0) cc_final: 0.8291 (t0) REVERT: E 50 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6925 (pt0) REVERT: F 84 MET cc_start: 0.8037 (tpp) cc_final: 0.7797 (mmm) REVERT: G 74 LYS cc_start: 0.7783 (tppt) cc_final: 0.7412 (mmmm) REVERT: G 95 LYS cc_start: 0.8473 (ttmm) cc_final: 0.8271 (tttm) REVERT: H 54 LYS cc_start: 0.8591 (tppt) cc_final: 0.8386 (mmmt) REVERT: K 764 PHE cc_start: 0.7797 (m-10) cc_final: 0.7378 (m-10) REVERT: K 918 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8272 (mm-30) REVERT: K 957 VAL cc_start: 0.8853 (t) cc_final: 0.8649 (t) REVERT: K 958 ASP cc_start: 0.7657 (m-30) cc_final: 0.7422 (m-30) REVERT: K 1208 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5303 (mp) REVERT: K 1293 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.8123 (t-90) REVERT: L 88 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7880 (mtp180) REVERT: L 105 ASN cc_start: 0.8526 (t0) cc_final: 0.8274 (t0) REVERT: L 288 MET cc_start: 0.8330 (ttp) cc_final: 0.8113 (ttp) REVERT: L 336 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7546 (mttt) REVERT: L 345 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7880 (mm-30) REVERT: M 280 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7677 (tp30) REVERT: M 310 LEU cc_start: 0.8640 (mt) cc_final: 0.8412 (mt) REVERT: M 313 SER cc_start: 0.8827 (p) cc_final: 0.8540 (p) REVERT: N 107 LYS cc_start: 0.8203 (mmtp) cc_final: 0.7921 (ttpt) REVERT: N 271 SER cc_start: 0.8743 (t) cc_final: 0.8518 (m) REVERT: N 292 ASP cc_start: 0.7881 (t0) cc_final: 0.7638 (t0) REVERT: N 331 ASN cc_start: 0.6156 (t0) cc_final: 0.5812 (t0) REVERT: N 393 GLN cc_start: 0.7979 (mt0) cc_final: 0.7451 (mp10) REVERT: N 515 GLN cc_start: 0.8354 (mt0) cc_final: 0.7733 (pp30) REVERT: P 538 LYS cc_start: 0.8582 (ptpt) cc_final: 0.8353 (pttt) REVERT: P 541 GLN cc_start: 0.8153 (mt0) cc_final: 0.7749 (mm-40) outliers start: 44 outliers final: 27 residues processed: 360 average time/residue: 0.4184 time to fit residues: 226.2729 Evaluate side-chains 342 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 309 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 35 ARG Chi-restraints excluded: chain C residue 101 THR 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 92 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 857 HIS Chi-restraints excluded: chain K residue 1191 LEU Chi-restraints excluded: chain K residue 1208 LEU Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain K residue 1293 HIS Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 555 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 206 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 157 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 202 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 ASN G 104 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 GLN M 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.184309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132074 restraints weight = 31952.180| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.90 r_work: 0.3376 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27503 Z= 0.171 Angle : 0.552 10.057 38570 Z= 0.312 Chirality : 0.038 0.202 4262 Planarity : 0.004 0.053 3721 Dihedral : 26.594 178.350 6332 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.19 % Allowed : 20.36 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2335 helix: 1.59 (0.15), residues: 1299 sheet: -0.53 (0.50), residues: 111 loop : -0.22 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K1151 HIS 0.003 0.001 HIS K 857 PHE 0.021 0.001 PHE K 723 TYR 0.022 0.002 TYR M 373 ARG 0.011 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 1394) hydrogen bonds : angle 3.40597 ( 3678) metal coordination : bond 0.01052 ( 17) metal coordination : angle 3.02245 ( 15) covalent geometry : bond 0.00394 (27486) covalent geometry : angle 0.54898 (38555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 2.307 Fit side-chains revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8652 (tt) cc_final: 0.8412 (tp) REVERT: A 87 SER cc_start: 0.8832 (m) cc_final: 0.8475 (p) REVERT: A 90 MET cc_start: 0.8359 (tpp) cc_final: 0.7709 (tpp) REVERT: A 94 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: B 91 LYS cc_start: 0.8683 (tttp) cc_final: 0.8223 (tttm) REVERT: B 93 GLN cc_start: 0.7351 (mm110) cc_final: 0.7067 (mm110) REVERT: C 73 ASN cc_start: 0.8433 (t0) cc_final: 0.7930 (t0) REVERT: D 31 LYS cc_start: 0.8395 (mttt) cc_final: 0.8119 (pttt) REVERT: D 65 ASP cc_start: 0.8740 (t0) cc_final: 0.8449 (t0) REVERT: E 41 TYR cc_start: 0.8871 (m-80) cc_final: 0.8291 (m-80) REVERT: E 42 ARG cc_start: 0.8158 (mtp85) cc_final: 0.7854 (mtt90) REVERT: E 50 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7041 (pt0) REVERT: F 84 MET cc_start: 0.8166 (tpp) cc_final: 0.7900 (mmm) REVERT: G 74 LYS cc_start: 0.7943 (tppt) cc_final: 0.7568 (mmmm) REVERT: H 54 LYS cc_start: 0.8617 (tppt) cc_final: 0.8409 (mmmt) REVERT: K 957 VAL cc_start: 0.8907 (t) cc_final: 0.8660 (t) REVERT: K 1129 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6494 (mm) REVERT: L 88 ARG cc_start: 0.8291 (mtp85) cc_final: 0.7980 (mtp180) REVERT: L 105 ASN cc_start: 0.8554 (t0) cc_final: 0.8332 (t0) REVERT: L 336 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7754 (mttt) REVERT: L 352 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8387 (mttp) REVERT: M 242 ASP cc_start: 0.8182 (m-30) cc_final: 0.7851 (m-30) REVERT: M 280 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7682 (tp30) REVERT: M 310 LEU cc_start: 0.8629 (mt) cc_final: 0.8404 (mt) REVERT: M 313 SER cc_start: 0.8861 (p) cc_final: 0.8587 (p) REVERT: M 395 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7659 (tt0) REVERT: N 107 LYS cc_start: 0.8284 (mmtp) cc_final: 0.7973 (ttpt) REVERT: N 271 SER cc_start: 0.8784 (t) cc_final: 0.8552 (m) REVERT: N 331 ASN cc_start: 0.6142 (t0) cc_final: 0.5787 (t0) REVERT: N 393 GLN cc_start: 0.8082 (mt0) cc_final: 0.7521 (mp10) REVERT: N 515 GLN cc_start: 0.8444 (mt0) cc_final: 0.7786 (pp30) REVERT: P 538 LYS cc_start: 0.8611 (ptpt) cc_final: 0.8381 (pttt) outliers start: 46 outliers final: 29 residues processed: 342 average time/residue: 0.4190 time to fit residues: 216.1206 Evaluate side-chains 339 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 304 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1129 ILE Chi-restraints excluded: chain K residue 1191 LEU Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 352 LYS Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 555 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 226 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 249 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 chunk 207 optimal weight: 30.0000 chunk 230 optimal weight: 6.9990 chunk 211 optimal weight: 0.0270 chunk 195 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.184247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131908 restraints weight = 31756.693| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.92 r_work: 0.3391 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27503 Z= 0.161 Angle : 0.547 10.040 38570 Z= 0.310 Chirality : 0.037 0.203 4262 Planarity : 0.004 0.053 3721 Dihedral : 26.564 178.722 6332 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.86 % Allowed : 20.46 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2335 helix: 1.58 (0.15), residues: 1300 sheet: -0.62 (0.49), residues: 113 loop : -0.18 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1151 HIS 0.003 0.001 HIS K 998 PHE 0.017 0.001 PHE H 67 TYR 0.017 0.001 TYR A 54 ARG 0.010 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 1394) hydrogen bonds : angle 3.42443 ( 3678) metal coordination : bond 0.00910 ( 17) metal coordination : angle 2.84306 ( 15) covalent geometry : bond 0.00369 (27486) covalent geometry : angle 0.54429 (38555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 310 time to evaluate : 2.460 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8320 (tpp) cc_final: 0.7647 (tpp) REVERT: A 94 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: B 91 LYS cc_start: 0.8660 (tttp) cc_final: 0.8246 (mtpp) REVERT: B 93 GLN cc_start: 0.7298 (mm110) cc_final: 0.7008 (mm110) REVERT: C 73 ASN cc_start: 0.8428 (t0) cc_final: 0.7925 (t0) REVERT: D 31 LYS cc_start: 0.8384 (mttt) cc_final: 0.8121 (pttt) REVERT: D 65 ASP cc_start: 0.8720 (t0) cc_final: 0.8277 (t0) REVERT: E 41 TYR cc_start: 0.8817 (m-80) cc_final: 0.8213 (m-80) REVERT: E 42 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7803 (mtt90) REVERT: E 50 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7027 (pt0) REVERT: F 84 MET cc_start: 0.8139 (tpp) cc_final: 0.7872 (mmm) REVERT: G 74 LYS cc_start: 0.7881 (tppt) cc_final: 0.7566 (mmmm) REVERT: H 54 LYS cc_start: 0.8588 (tppt) cc_final: 0.8376 (mmmt) REVERT: K 957 VAL cc_start: 0.8890 (t) cc_final: 0.8648 (t) REVERT: K 958 ASP cc_start: 0.7664 (m-30) cc_final: 0.7410 (m-30) REVERT: K 1129 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6515 (mm) REVERT: K 1208 LEU cc_start: 0.6573 (mt) cc_final: 0.5786 (mp) REVERT: L 88 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7939 (mtp180) REVERT: L 336 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7699 (mtpt) REVERT: L 352 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8421 (mttp) REVERT: M 242 ASP cc_start: 0.8168 (m-30) cc_final: 0.7833 (m-30) REVERT: M 280 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7698 (tp30) REVERT: M 310 LEU cc_start: 0.8604 (mt) cc_final: 0.8368 (mt) REVERT: M 313 SER cc_start: 0.8854 (p) cc_final: 0.8582 (p) REVERT: M 395 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: N 107 LYS cc_start: 0.8285 (mmtp) cc_final: 0.7987 (ttpt) REVERT: N 271 SER cc_start: 0.8772 (t) cc_final: 0.8544 (m) REVERT: N 331 ASN cc_start: 0.6327 (t0) cc_final: 0.5948 (t0) REVERT: N 393 GLN cc_start: 0.8068 (mt0) cc_final: 0.7502 (mp10) REVERT: N 515 GLN cc_start: 0.8446 (mt0) cc_final: 0.7774 (pp30) REVERT: P 538 LYS cc_start: 0.8618 (ptpt) cc_final: 0.8367 (pttt) outliers start: 39 outliers final: 28 residues processed: 334 average time/residue: 0.4330 time to fit residues: 217.7761 Evaluate side-chains 340 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 305 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 1129 ILE Chi-restraints excluded: chain K residue 1191 LEU Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 352 LYS Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 555 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 250 optimal weight: 5.9990 chunk 211 optimal weight: 0.0070 chunk 155 optimal weight: 0.6980 chunk 249 optimal weight: 5.9990 chunk 74 optimal weight: 80.0000 chunk 196 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.184728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132318 restraints weight = 31923.640| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.86 r_work: 0.3429 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27503 Z= 0.150 Angle : 0.538 9.390 38570 Z= 0.306 Chirality : 0.037 0.195 4262 Planarity : 0.004 0.053 3721 Dihedral : 26.529 178.839 6332 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.05 % Allowed : 20.41 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2335 helix: 1.60 (0.15), residues: 1302 sheet: -0.52 (0.49), residues: 113 loop : -0.14 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K1151 HIS 0.003 0.001 HIS K 998 PHE 0.017 0.001 PHE H 67 TYR 0.017 0.001 TYR A 54 ARG 0.010 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 1394) hydrogen bonds : angle 3.40282 ( 3678) metal coordination : bond 0.00849 ( 17) metal coordination : angle 2.80769 ( 15) covalent geometry : bond 0.00341 (27486) covalent geometry : angle 0.53570 (38555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17261.39 seconds wall clock time: 297 minutes 26.76 seconds (17846.76 seconds total)