Starting phenix.real_space_refine on Mon Aug 25 06:31:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxy_35082/08_2025/8hxy_35082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxy_35082/08_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_35082/08_2025/8hxy_35082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxy_35082/08_2025/8hxy_35082.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxy_35082/08_2025/8hxy_35082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxy_35082/08_2025/8hxy_35082.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.70, per 1000 atoms: 0.18 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: 1.76 Conformation dependent library (CDL) restraints added in 758.7 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 2.87 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: 7.80 Time building geometry restraints manager: 2.29 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 28.180 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.001 ARG N 369 TYR 0.033 0.002 TYR A 99 PHE 0.039 0.002 PHE N 311 TRP 0.021 0.002 TRP K1223 HIS 0.008 0.001 HIS N 469 Details of bonding type rmsd covalent geometry : bond 0.00679 (27486) covalent geometry : angle 0.94094 (38555) hydrogen bonds : bond 0.15642 ( 1394) hydrogen bonds : angle 6.63483 ( 3678) metal coordination : bond 0.00768 ( 17) metal coordination : angle 3.24015 ( 15) *********************** 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 : 0.771 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: 0.1845 time to fit residues: 158.0640 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 : 0.801 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0970 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 68 ASN C 73 ASN C 112 GLN D 92 GLN ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 GLN P 541 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.193823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142958 restraints weight = 32468.858| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.02 r_work: 0.3546 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2009 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= 0.147 Angle : 0.568 8.239 38570 Z= 0.323 Chirality : 0.037 0.187 4262 Planarity : 0.005 0.080 3721 Dihedral : 26.818 177.635 6335 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.43 % Allowed : 17.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.17), residues: 2335 helix: 0.30 (0.14), residues: 1277 sheet: -0.34 (0.47), residues: 121 loop : -0.70 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 757 TYR 0.027 0.001 TYR H 80 PHE 0.018 0.001 PHE K 668 TRP 0.010 0.001 TRP N 129 HIS 0.004 0.001 HIS N 430 Details of bonding type rmsd covalent geometry : bond 0.00318 (27486) covalent geometry : angle 0.56454 (38555) hydrogen bonds : bond 0.03979 ( 1394) hydrogen bonds : angle 3.93842 ( 3678) metal coordination : bond 0.00769 ( 17) metal coordination : angle 3.25249 ( 15) *********************** 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 454 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 403 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8089 (tp) REVERT: A 87 SER cc_start: 0.9053 (t) cc_final: 0.8687 (p) REVERT: A 129 ARG cc_start: 0.8228 (tpt90) cc_final: 0.7739 (tpt90) REVERT: B 31 LYS cc_start: 0.8546 (tttt) cc_final: 0.8236 (tttt) REVERT: B 35 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.8225 (mtp-110) REVERT: B 91 LYS cc_start: 0.8603 (mtpp) cc_final: 0.8366 (tttp) REVERT: B 93 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7428 (mp10) REVERT: C 99 ARG cc_start: 0.7298 (ptm160) cc_final: 0.7059 (mtp85) REVERT: D 65 ASP cc_start: 0.8723 (t0) cc_final: 0.8397 (t0) REVERT: E 56 LYS cc_start: 0.9055 (ttpp) cc_final: 0.8663 (ttpp) REVERT: F 74 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: F 79 LYS cc_start: 0.8107 (mttp) cc_final: 0.7775 (mmtm) REVERT: H 32 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6870 (mt-10) REVERT: H 76 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7703 (ttm110) REVERT: H 83 ARG cc_start: 0.8055 (mmt90) cc_final: 0.7826 (mmp80) REVERT: H 96 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7771 (ttp-110) REVERT: K 668 PHE cc_start: 0.7774 (t80) cc_final: 0.7454 (t80) REVERT: K 695 ASP cc_start: 0.7768 (m-30) cc_final: 0.7424 (t0) REVERT: K 714 LYS cc_start: 0.8027 (mmtp) cc_final: 0.7752 (mtmm) REVERT: K 764 PHE cc_start: 0.7456 (m-10) cc_final: 0.6913 (m-10) REVERT: K 812 GLU cc_start: 0.7811 (tp30) cc_final: 0.7475 (tp30) REVERT: K 903 GLU cc_start: 0.7658 (pp20) cc_final: 0.7416 (pt0) REVERT: K 958 ASP cc_start: 0.7937 (m-30) cc_final: 0.7731 (m-30) REVERT: K 1205 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7868 (mttt) REVERT: K 1227 SER cc_start: 0.8827 (t) cc_final: 0.8516 (p) REVERT: K 1287 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7682 (ttp80) REVERT: L 53 MET cc_start: 0.8692 (mmp) cc_final: 0.8389 (mmm) REVERT: L 100 GLU cc_start: 0.8234 (mp0) cc_final: 0.7908 (mt-10) REVERT: L 136 ARG cc_start: 0.8514 (mtp85) cc_final: 0.8131 (mtt-85) REVERT: L 248 ARG cc_start: 0.8054 (ttt180) cc_final: 0.7788 (ttt-90) REVERT: M 395 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: N 107 LYS cc_start: 0.8322 (mmtp) cc_final: 0.8110 (ttpt) REVERT: N 113 LEU cc_start: 0.8541 (mm) cc_final: 0.8054 (mp) REVERT: N 117 LYS cc_start: 0.8060 (mmtp) cc_final: 0.7746 (mmmt) REVERT: N 187 TRP cc_start: 0.6471 (m100) cc_final: 0.6262 (m100) REVERT: N 261 ASP cc_start: 0.8374 (m-30) cc_final: 0.8118 (m-30) REVERT: N 291 ILE cc_start: 0.7977 (mm) cc_final: 0.7671 (mt) REVERT: N 375 GLU cc_start: 0.8328 (pt0) cc_final: 0.8016 (pm20) REVERT: N 505 TYR cc_start: 0.7650 (m-80) cc_final: 0.7298 (m-80) REVERT: N 512 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7736 (mm) REVERT: N 517 ASN cc_start: 0.6932 (t0) cc_final: 0.6723 (t0) outliers start: 51 outliers final: 18 residues processed: 434 average time/residue: 0.1661 time to fit residues: 108.2840 Evaluate side-chains 368 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 346 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 ILE 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 D residue 49 THR Chi-restraints excluded: chain D residue 87 THR 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 H residue 115 VAL Chi-restraints excluded: chain K residue 857 HIS 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 390 THR 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 Chi-restraints excluded: chain N residue 512 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 87 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 162 optimal weight: 0.0570 chunk 64 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN D 81 ASN E 19 GLN E 39 HIS E 68 GLN E 93 GLN G 104 GLN ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.184734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.131344 restraints weight = 32040.169| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.87 r_work: 0.3378 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27503 Z= 0.206 Angle : 0.597 7.363 38570 Z= 0.335 Chirality : 0.040 0.192 4262 Planarity : 0.005 0.065 3721 Dihedral : 27.006 177.235 6332 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.71 % Allowed : 17.84 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.17), residues: 2335 helix: 0.91 (0.14), residues: 1283 sheet: -0.35 (0.47), residues: 121 loop : -0.53 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 19 TYR 0.035 0.002 TYR F 88 PHE 0.016 0.002 PHE L 24 TRP 0.013 0.001 TRP K1151 HIS 0.007 0.001 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00477 (27486) covalent geometry : angle 0.59298 (38555) hydrogen bonds : bond 0.04006 ( 1394) hydrogen bonds : angle 3.68432 ( 3678) metal coordination : bond 0.01206 ( 17) metal coordination : angle 3.44090 ( 15) *********************** 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 418 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 361 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 87 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8748 (m) REVERT: A 94 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8230 (mp0) REVERT: A 129 ARG cc_start: 0.8546 (tpt90) cc_final: 0.8010 (tpt90) REVERT: B 31 LYS cc_start: 0.8529 (tttt) cc_final: 0.8281 (tttt) REVERT: B 35 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8173 (mtp-110) REVERT: B 93 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7475 (mp10) REVERT: C 73 ASN cc_start: 0.8324 (t0) cc_final: 0.7872 (t0) REVERT: D 65 ASP cc_start: 0.8883 (t0) cc_final: 0.8574 (t0) REVERT: D 81 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8363 (m110) REVERT: F 79 LYS cc_start: 0.8233 (mttp) cc_final: 0.7919 (mmtm) REVERT: F 84 MET cc_start: 0.8286 (tpp) cc_final: 0.7928 (mmm) REVERT: G 74 LYS cc_start: 0.7810 (tppt) cc_final: 0.7312 (mmmm) REVERT: G 95 LYS cc_start: 0.8461 (tttp) cc_final: 0.8171 (ttmm) REVERT: H 54 LYS cc_start: 0.8677 (tppt) cc_final: 0.8404 (mmmt) REVERT: H 83 ARG cc_start: 0.8093 (mmt90) cc_final: 0.7866 (mmp80) REVERT: K 714 LYS cc_start: 0.8042 (mmtp) cc_final: 0.7828 (mtmm) REVERT: K 726 TYR cc_start: 0.6651 (t80) cc_final: 0.6405 (t80) REVERT: K 812 GLU cc_start: 0.7926 (tp30) cc_final: 0.7568 (tp30) REVERT: K 841 MET cc_start: 0.5115 (ptt) cc_final: 0.4645 (ptt) REVERT: K 957 VAL cc_start: 0.8891 (t) cc_final: 0.8612 (t) REVERT: L 53 MET cc_start: 0.8776 (mmp) cc_final: 0.8533 (mmm) REVERT: L 72 GLN cc_start: 0.8479 (tt0) cc_final: 0.8140 (tt0) REVERT: M 280 GLU cc_start: 0.8269 (tp30) cc_final: 0.8028 (tp30) REVERT: M 310 LEU cc_start: 0.8571 (mt) cc_final: 0.8338 (mt) REVERT: M 313 SER cc_start: 0.8729 (p) cc_final: 0.8511 (p) REVERT: M 375 ASN cc_start: 0.7904 (p0) cc_final: 0.7647 (p0) REVERT: M 395 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: N 107 LYS cc_start: 0.8528 (mmtp) cc_final: 0.8271 (ttpt) REVERT: N 261 ASP cc_start: 0.8500 (m-30) cc_final: 0.8171 (m-30) REVERT: N 271 SER cc_start: 0.8799 (t) cc_final: 0.8538 (m) REVERT: N 291 ILE cc_start: 0.8312 (mm) cc_final: 0.8099 (mt) REVERT: N 393 GLN cc_start: 0.8314 (mt0) cc_final: 0.7561 (mp10) outliers start: 57 outliers final: 29 residues processed: 400 average time/residue: 0.1708 time to fit residues: 101.7402 Evaluate side-chains 352 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 319 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER 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 61 SER Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain E residue 14 LYS 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 84 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 1250 VAL 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 160 PHE 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 380 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 20 optimal weight: 0.8980 chunk 235 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 212 optimal weight: 0.8980 chunk 37 optimal weight: 40.0000 chunk 168 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 90 optimal weight: 30.0000 chunk 190 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 GLN N 517 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.185016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132782 restraints weight = 31794.652| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.79 r_work: 0.3393 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27503 Z= 0.168 Angle : 0.548 10.651 38570 Z= 0.310 Chirality : 0.037 0.159 4262 Planarity : 0.004 0.055 3721 Dihedral : 26.788 178.032 6332 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.38 % Allowed : 18.13 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.17), residues: 2335 helix: 1.25 (0.15), residues: 1283 sheet: -0.28 (0.48), residues: 122 loop : -0.41 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 53 TYR 0.016 0.002 TYR F 88 PHE 0.014 0.001 PHE E 67 TRP 0.010 0.001 TRP K1151 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00384 (27486) covalent geometry : angle 0.54446 (38555) hydrogen bonds : bond 0.03607 ( 1394) hydrogen bonds : angle 3.51063 ( 3678) metal coordination : bond 0.00861 ( 17) metal coordination : angle 3.03845 ( 15) *********************** 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 390 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 340 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 87 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8746 (m) REVERT: B 31 LYS cc_start: 0.8535 (tttt) cc_final: 0.8239 (tttt) REVERT: B 35 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.8121 (mtp-110) REVERT: B 93 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7561 (mm110) REVERT: C 35 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7807 (mtm-85) REVERT: C 73 ASN cc_start: 0.8414 (t0) cc_final: 0.7921 (t0) REVERT: D 65 ASP cc_start: 0.8752 (t0) cc_final: 0.8458 (t0) REVERT: E 50 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7163 (pt0) REVERT: F 84 MET cc_start: 0.8182 (tpp) cc_final: 0.7869 (mmm) REVERT: G 41 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7634 (mt-10) REVERT: G 74 LYS cc_start: 0.7837 (tppt) cc_final: 0.7486 (mmmm) REVERT: G 95 LYS cc_start: 0.8441 (tttp) cc_final: 0.8139 (ttmm) REVERT: H 54 LYS cc_start: 0.8645 (tppt) cc_final: 0.8394 (mmmt) REVERT: H 83 ARG cc_start: 0.8048 (mmt90) cc_final: 0.7831 (mpt180) REVERT: K 668 PHE cc_start: 0.7912 (t80) cc_final: 0.7660 (t80) REVERT: K 714 LYS cc_start: 0.8013 (mmtp) cc_final: 0.7806 (mtmm) REVERT: K 812 GLU cc_start: 0.7936 (tp30) cc_final: 0.7539 (tp30) REVERT: K 841 MET cc_start: 0.5128 (ptt) cc_final: 0.4647 (ptt) REVERT: K 927 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8535 (p) REVERT: K 957 VAL cc_start: 0.8855 (t) cc_final: 0.8583 (t) REVERT: K 1208 LEU cc_start: 0.6303 (mt) cc_final: 0.5861 (mp) REVERT: L 72 GLN cc_start: 0.8486 (tt0) cc_final: 0.8131 (tt0) REVERT: L 316 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7447 (ptt-90) REVERT: M 310 LEU cc_start: 0.8608 (mt) cc_final: 0.8354 (mt) REVERT: M 313 SER cc_start: 0.8740 (p) cc_final: 0.8525 (p) REVERT: M 395 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: N 107 LYS cc_start: 0.8493 (mmtp) cc_final: 0.8180 (ttpt) REVERT: N 271 SER cc_start: 0.8766 (t) cc_final: 0.8529 (m) REVERT: N 393 GLN cc_start: 0.8255 (mt0) cc_final: 0.7573 (mp10) REVERT: P 538 LYS cc_start: 0.8524 (ptpt) cc_final: 0.8206 (pttt) outliers start: 50 outliers final: 32 residues processed: 373 average time/residue: 0.1654 time to fit residues: 93.4631 Evaluate side-chains 348 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 310 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 95 LYS 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 D residue 87 THR 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 H residue 115 VAL Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 927 SER Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 160 PHE Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 316 ARG Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 245 ILE Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 295 ASN 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 294 ASN Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 162 optimal weight: 0.0000 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 ASN H 46 HIS H 81 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.187068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.135240 restraints weight = 31834.493| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.86 r_work: 0.3451 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3449 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= 0.135 Angle : 0.521 11.388 38570 Z= 0.297 Chirality : 0.036 0.183 4262 Planarity : 0.004 0.052 3721 Dihedral : 26.596 178.427 6332 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.47 % Allowed : 18.08 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.18), residues: 2335 helix: 1.51 (0.15), residues: 1285 sheet: -0.20 (0.48), residues: 122 loop : -0.32 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 496 TYR 0.015 0.001 TYR N 514 PHE 0.013 0.001 PHE A 67 TRP 0.007 0.001 TRP K1151 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00300 (27486) covalent geometry : angle 0.51778 (38555) hydrogen bonds : bond 0.03361 ( 1394) hydrogen bonds : angle 3.36763 ( 3678) metal coordination : bond 0.00689 ( 17) metal coordination : angle 2.79732 ( 15) *********************** 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 389 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 337 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 87 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8658 (p) REVERT: A 129 ARG cc_start: 0.8490 (tpt90) cc_final: 0.8146 (tpt90) REVERT: B 31 LYS cc_start: 0.8520 (tttt) cc_final: 0.8251 (tttt) REVERT: B 35 ARG cc_start: 0.8375 (ttm-80) cc_final: 0.8124 (mtp-110) REVERT: B 93 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7415 (mm110) REVERT: C 73 ASN cc_start: 0.8474 (t0) cc_final: 0.7988 (t0) REVERT: D 68 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7603 (mt-10) REVERT: E 50 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7066 (pt0) REVERT: E 79 LYS cc_start: 0.8380 (tttp) cc_final: 0.7928 (tttp) REVERT: F 84 MET cc_start: 0.8150 (tpp) cc_final: 0.7918 (mmm) REVERT: G 41 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7661 (mt-10) REVERT: G 74 LYS cc_start: 0.7882 (tppt) cc_final: 0.7456 (mmmm) REVERT: G 95 LYS cc_start: 0.8438 (tttp) cc_final: 0.8160 (ttmm) REVERT: H 54 LYS cc_start: 0.8614 (tppt) cc_final: 0.8363 (mmmt) REVERT: H 83 ARG cc_start: 0.7975 (mmt90) cc_final: 0.7749 (mpt180) REVERT: K 668 PHE cc_start: 0.7960 (t80) cc_final: 0.7725 (t80) REVERT: K 714 LYS cc_start: 0.8061 (mmtp) cc_final: 0.7840 (mtmm) REVERT: K 763 THR cc_start: 0.7903 (m) cc_final: 0.7511 (p) REVERT: K 812 GLU cc_start: 0.7899 (tp30) cc_final: 0.7636 (tp30) REVERT: K 841 MET cc_start: 0.5162 (ptt) cc_final: 0.4670 (ptt) REVERT: K 927 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8509 (p) REVERT: K 957 VAL cc_start: 0.8850 (t) cc_final: 0.8604 (t) REVERT: K 958 ASP cc_start: 0.7596 (m-30) cc_final: 0.7254 (m-30) REVERT: L 53 MET cc_start: 0.8605 (mmt) cc_final: 0.8378 (mmm) REVERT: L 72 GLN cc_start: 0.8407 (tt0) cc_final: 0.8040 (tt0) REVERT: L 335 ASP cc_start: 0.7883 (p0) cc_final: 0.7354 (p0) REVERT: M 275 GLN cc_start: 0.7662 (mm110) cc_final: 0.7442 (mm110) REVERT: M 310 LEU cc_start: 0.8617 (mt) cc_final: 0.8374 (mt) REVERT: M 313 SER cc_start: 0.8749 (p) cc_final: 0.8521 (p) REVERT: M 395 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: N 107 LYS cc_start: 0.8445 (mmtp) cc_final: 0.8146 (ttpt) REVERT: N 271 SER cc_start: 0.8771 (t) cc_final: 0.8527 (m) REVERT: N 393 GLN cc_start: 0.8185 (mt0) cc_final: 0.7659 (mp10) REVERT: P 538 LYS cc_start: 0.8546 (ptpt) cc_final: 0.8331 (pttt) outliers start: 52 outliers final: 28 residues processed: 373 average time/residue: 0.1609 time to fit residues: 90.8342 Evaluate side-chains 343 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 311 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 100 VAL 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 115 VAL Chi-restraints excluded: chain K residue 858 THR Chi-restraints excluded: chain K residue 903 GLU Chi-restraints excluded: chain K residue 927 SER Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1196 LEU Chi-restraints excluded: chain K residue 1295 SER Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 160 PHE Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 245 ILE Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 368 MET Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN M 125 GLN M 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.186755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.134661 restraints weight = 31955.550| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.83 r_work: 0.3423 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3611 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= 0.140 Angle : 0.526 11.748 38570 Z= 0.299 Chirality : 0.037 0.210 4262 Planarity : 0.004 0.051 3721 Dihedral : 26.534 178.428 6332 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.85 % Allowed : 18.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.17), residues: 2335 helix: 1.59 (0.15), residues: 1298 sheet: -0.32 (0.50), residues: 108 loop : -0.24 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 88 TYR 0.015 0.001 TYR L 313 PHE 0.013 0.001 PHE A 67 TRP 0.007 0.001 TRP K1151 HIS 0.003 0.001 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00312 (27486) covalent geometry : angle 0.52320 (38555) hydrogen bonds : bond 0.03367 ( 1394) hydrogen bonds : angle 3.32999 ( 3678) metal coordination : bond 0.00730 ( 17) metal coordination : angle 2.74022 ( 15) *********************** 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 385 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8685 (p) REVERT: A 129 ARG cc_start: 0.8509 (tpt90) cc_final: 0.8131 (tpt90) REVERT: B 31 LYS cc_start: 0.8544 (tttt) cc_final: 0.8261 (tttt) REVERT: B 35 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8108 (mtp-110) REVERT: B 93 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7354 (mm110) REVERT: C 73 ASN cc_start: 0.8471 (t0) cc_final: 0.7950 (t0) REVERT: E 41 TYR cc_start: 0.8836 (m-80) cc_final: 0.8266 (m-80) REVERT: E 50 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7094 (pt0) REVERT: F 84 MET cc_start: 0.8186 (tpp) cc_final: 0.7915 (mmm) REVERT: G 74 LYS cc_start: 0.7858 (tppt) cc_final: 0.7416 (mmmm) REVERT: H 54 LYS cc_start: 0.8650 (tppt) cc_final: 0.8430 (mmmt) REVERT: H 83 ARG cc_start: 0.8010 (mmt90) cc_final: 0.7720 (mpt180) REVERT: K 668 PHE cc_start: 0.7957 (t80) cc_final: 0.7717 (t80) REVERT: K 714 LYS cc_start: 0.8078 (mmtp) cc_final: 0.7804 (mtmm) REVERT: K 763 THR cc_start: 0.7840 (m) cc_final: 0.7444 (p) REVERT: K 812 GLU cc_start: 0.7949 (tp30) cc_final: 0.7663 (tp30) REVERT: K 841 MET cc_start: 0.5064 (ptt) cc_final: 0.4631 (ptt) REVERT: K 927 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8501 (p) REVERT: K 957 VAL cc_start: 0.8855 (t) cc_final: 0.8606 (t) REVERT: K 958 ASP cc_start: 0.7616 (m-30) cc_final: 0.7334 (m-30) REVERT: L 72 GLN cc_start: 0.8487 (tt0) cc_final: 0.8191 (tt0) REVERT: L 88 ARG cc_start: 0.8393 (mtp85) cc_final: 0.8091 (mtp180) REVERT: M 275 GLN cc_start: 0.7683 (mm110) cc_final: 0.7464 (mm110) REVERT: M 310 LEU cc_start: 0.8614 (mt) cc_final: 0.8366 (mt) REVERT: M 313 SER cc_start: 0.8739 (p) cc_final: 0.8489 (p) REVERT: N 107 LYS cc_start: 0.8429 (mmtp) cc_final: 0.8105 (ttpt) REVERT: N 271 SER cc_start: 0.8773 (t) cc_final: 0.8546 (m) REVERT: N 375 GLU cc_start: 0.8200 (pt0) cc_final: 0.7924 (pm20) REVERT: N 393 GLN cc_start: 0.7983 (mt0) cc_final: 0.7414 (mp10) REVERT: P 538 LYS cc_start: 0.8580 (ptpt) cc_final: 0.8378 (pttt) outliers start: 60 outliers final: 38 residues processed: 369 average time/residue: 0.1606 time to fit residues: 90.0335 Evaluate side-chains 350 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 309 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER 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 101 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 115 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 858 THR Chi-restraints excluded: chain K residue 903 GLU Chi-restraints excluded: chain K residue 927 SER Chi-restraints excluded: chain K residue 973 SER Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1196 LEU Chi-restraints excluded: chain K residue 1208 LEU Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1295 SER Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 160 PHE Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 125 GLN Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 372 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 Chi-restraints excluded: chain P residue 545 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 21 optimal weight: 2.9990 chunk 244 optimal weight: 0.0270 chunk 252 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 211 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 chunk 238 optimal weight: 0.8980 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN L 38 HIS M 330 HIS M 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.185335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133060 restraints weight = 31701.839| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.84 r_work: 0.3427 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27503 Z= 0.160 Angle : 0.542 10.537 38570 Z= 0.306 Chirality : 0.037 0.206 4262 Planarity : 0.004 0.050 3721 Dihedral : 26.564 178.346 6332 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.66 % Allowed : 18.74 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.17), residues: 2335 helix: 1.58 (0.15), residues: 1302 sheet: -0.29 (0.51), residues: 106 loop : -0.26 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 496 TYR 0.023 0.001 TYR K 726 PHE 0.023 0.001 PHE K1022 TRP 0.009 0.001 TRP K1151 HIS 0.004 0.001 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00367 (27486) covalent geometry : angle 0.53924 (38555) hydrogen bonds : bond 0.03493 ( 1394) hydrogen bonds : angle 3.36454 ( 3678) metal coordination : bond 0.00857 ( 17) metal coordination : angle 2.84134 ( 15) *********************** 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 378 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 322 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8969 (OUTLIER) cc_final: 0.8700 (p) REVERT: A 129 ARG cc_start: 0.8531 (tpt90) cc_final: 0.8299 (tpt-90) REVERT: B 31 LYS cc_start: 0.8556 (tttt) cc_final: 0.8258 (tttt) REVERT: B 35 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.8150 (mtp-110) REVERT: B 93 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7316 (mm110) REVERT: C 73 ASN cc_start: 0.8453 (t0) cc_final: 0.7939 (t0) REVERT: E 50 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6945 (pt0) REVERT: E 79 LYS cc_start: 0.8388 (tttp) cc_final: 0.7969 (tttp) REVERT: F 84 MET cc_start: 0.8185 (tpp) cc_final: 0.7936 (mmm) REVERT: G 74 LYS cc_start: 0.7907 (tppt) cc_final: 0.7517 (mmmm) REVERT: H 54 LYS cc_start: 0.8663 (tppt) cc_final: 0.8421 (mmmt) REVERT: H 83 ARG cc_start: 0.8013 (mmt90) cc_final: 0.7804 (mpt180) REVERT: K 674 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7704 (ttp-110) REVERT: K 714 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7841 (mtmm) REVERT: K 719 TRP cc_start: 0.8574 (t-100) cc_final: 0.7920 (t60) REVERT: K 763 THR cc_start: 0.7947 (m) cc_final: 0.7575 (p) REVERT: K 812 GLU cc_start: 0.7911 (tp30) cc_final: 0.7582 (tp30) REVERT: K 841 MET cc_start: 0.5137 (ptt) cc_final: 0.4643 (ptt) REVERT: K 927 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8481 (p) REVERT: K 957 VAL cc_start: 0.8880 (t) cc_final: 0.8630 (t) REVERT: K 958 ASP cc_start: 0.7628 (m-30) cc_final: 0.7336 (m-30) REVERT: L 336 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7797 (mtpt) REVERT: M 275 GLN cc_start: 0.7668 (mm110) cc_final: 0.7463 (mm110) REVERT: M 310 LEU cc_start: 0.8616 (mt) cc_final: 0.8383 (mt) REVERT: M 313 SER cc_start: 0.8878 (p) cc_final: 0.8621 (p) REVERT: M 395 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: N 107 LYS cc_start: 0.8354 (mmtp) cc_final: 0.8072 (ttpt) REVERT: N 271 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8572 (m) REVERT: N 375 GLU cc_start: 0.8179 (pt0) cc_final: 0.7872 (pm20) REVERT: N 393 GLN cc_start: 0.8053 (mt0) cc_final: 0.7517 (mp10) REVERT: P 538 LYS cc_start: 0.8601 (ptpt) cc_final: 0.8390 (pttt) outliers start: 56 outliers final: 41 residues processed: 359 average time/residue: 0.1860 time to fit residues: 100.7138 Evaluate side-chains 359 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 312 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER 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 61 SER 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 115 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 818 ASP Chi-restraints excluded: chain K residue 858 THR Chi-restraints excluded: chain K residue 903 GLU Chi-restraints excluded: chain K residue 927 SER Chi-restraints excluded: chain K residue 973 SER Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1196 LEU Chi-restraints excluded: chain K residue 1250 VAL 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 155 SER Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 160 PHE Chi-restraints excluded: chain L residue 205 THR 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 292 CYS Chi-restraints excluded: chain M residue 295 ASN 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 271 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 338 LYS Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 231 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 169 optimal weight: 0.0470 chunk 185 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 249 optimal weight: 0.0020 chunk 122 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 247 optimal weight: 0.0270 chunk 220 optimal weight: 3.9990 overall best weight: 0.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 353 GLN P 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.189844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138315 restraints weight = 32085.346| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.99 r_work: 0.3452 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3860 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= 0.122 Angle : 0.516 9.870 38570 Z= 0.293 Chirality : 0.036 0.208 4262 Planarity : 0.004 0.052 3721 Dihedral : 26.327 179.027 6332 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.09 % Allowed : 19.51 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.18), residues: 2335 helix: 1.83 (0.15), residues: 1295 sheet: -0.28 (0.50), residues: 108 loop : -0.19 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 324 TYR 0.022 0.001 TYR K 726 PHE 0.019 0.001 PHE K1305 TRP 0.006 0.001 TRP N 301 HIS 0.003 0.001 HIS K 998 Details of bonding type rmsd covalent geometry : bond 0.00263 (27486) covalent geometry : angle 0.51379 (38555) hydrogen bonds : bond 0.03227 ( 1394) hydrogen bonds : angle 3.27329 ( 3678) metal coordination : bond 0.00622 ( 17) metal coordination : angle 2.56403 ( 15) *********************** 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 374 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 330 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8535 (p) REVERT: A 129 ARG cc_start: 0.8256 (tpt90) cc_final: 0.8045 (tpt-90) REVERT: B 31 LYS cc_start: 0.8460 (tttt) cc_final: 0.8133 (tttt) REVERT: B 35 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7934 (mtp-110) REVERT: C 73 ASN cc_start: 0.8360 (t0) cc_final: 0.7940 (t0) REVERT: D 68 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7312 (mt-10) REVERT: E 41 TYR cc_start: 0.8745 (m-80) cc_final: 0.7979 (m-80) REVERT: E 42 ARG cc_start: 0.7923 (mtp85) cc_final: 0.7533 (mtt90) REVERT: E 50 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6837 (pt0) REVERT: E 79 LYS cc_start: 0.8211 (tttp) cc_final: 0.7909 (tttp) REVERT: F 64 ASN cc_start: 0.7917 (m-40) cc_final: 0.7710 (m110) REVERT: F 84 MET cc_start: 0.7792 (tpp) cc_final: 0.7582 (mmm) REVERT: G 74 LYS cc_start: 0.7873 (tppt) cc_final: 0.7496 (mmmm) REVERT: G 95 LYS cc_start: 0.8386 (tttp) cc_final: 0.8078 (ttmm) REVERT: H 54 LYS cc_start: 0.8464 (tppt) cc_final: 0.8245 (mmmt) REVERT: K 668 PHE cc_start: 0.7754 (t80) cc_final: 0.7493 (t80) REVERT: K 674 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7590 (ttp-110) REVERT: K 696 ILE cc_start: 0.7602 (mt) cc_final: 0.7351 (mt) REVERT: K 714 LYS cc_start: 0.7951 (mmtp) cc_final: 0.7695 (mtmm) REVERT: K 763 THR cc_start: 0.7879 (m) cc_final: 0.7489 (p) REVERT: K 841 MET cc_start: 0.4876 (ptt) cc_final: 0.4533 (ptt) REVERT: K 927 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8424 (p) REVERT: K 957 VAL cc_start: 0.8851 (t) cc_final: 0.8643 (t) REVERT: L 336 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7514 (mttt) REVERT: M 310 LEU cc_start: 0.8549 (mt) cc_final: 0.8327 (mt) REVERT: M 313 SER cc_start: 0.8789 (p) cc_final: 0.8489 (p) REVERT: M 395 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: N 107 LYS cc_start: 0.8263 (mmtp) cc_final: 0.7995 (ttpt) REVERT: N 271 SER cc_start: 0.8631 (t) cc_final: 0.8419 (m) REVERT: N 375 GLU cc_start: 0.8043 (pt0) cc_final: 0.7809 (pm20) REVERT: N 393 GLN cc_start: 0.7851 (mt0) cc_final: 0.7378 (mp10) REVERT: N 515 GLN cc_start: 0.8004 (mt0) cc_final: 0.7188 (pp30) REVERT: P 538 LYS cc_start: 0.8501 (ptpt) cc_final: 0.8287 (pttt) REVERT: P 541 GLN cc_start: 0.7980 (mt0) cc_final: 0.7648 (mm-40) outliers start: 44 outliers final: 31 residues processed: 358 average time/residue: 0.1850 time to fit residues: 99.8926 Evaluate side-chains 358 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 322 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 87 SER 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 49 THR Chi-restraints excluded: chain D residue 61 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 G residue 27 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 818 ASP Chi-restraints excluded: chain K residue 858 THR Chi-restraints excluded: chain K residue 927 SER Chi-restraints excluded: chain K residue 973 SER Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1208 LEU 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 160 PHE 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 295 ASN Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 265 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 259 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 38 ASN G 104 GLN M 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.185073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132865 restraints weight = 31791.413| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.80 r_work: 0.3426 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27503 Z= 0.168 Angle : 0.550 9.638 38570 Z= 0.309 Chirality : 0.038 0.201 4262 Planarity : 0.004 0.051 3721 Dihedral : 26.530 178.250 6332 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.33 % Allowed : 19.65 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.17), residues: 2335 helix: 1.69 (0.15), residues: 1300 sheet: -0.26 (0.50), residues: 108 loop : -0.19 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 324 TYR 0.023 0.002 TYR K 726 PHE 0.030 0.001 PHE K1022 TRP 0.013 0.001 TRP K1151 HIS 0.004 0.001 HIS K 998 Details of bonding type rmsd covalent geometry : bond 0.00387 (27486) covalent geometry : angle 0.54724 (38555) hydrogen bonds : bond 0.03525 ( 1394) hydrogen bonds : angle 3.37476 ( 3678) metal coordination : bond 0.00947 ( 17) metal coordination : angle 2.92239 ( 15) *********************** 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 372 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 323 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8965 (OUTLIER) cc_final: 0.8688 (p) REVERT: A 129 ARG cc_start: 0.8444 (tpt90) cc_final: 0.8214 (tpt-90) REVERT: B 31 LYS cc_start: 0.8531 (tttt) cc_final: 0.8297 (tttt) REVERT: B 35 ARG cc_start: 0.8432 (ttm-80) cc_final: 0.8189 (mmm-85) REVERT: C 73 ASN cc_start: 0.8342 (t0) cc_final: 0.7890 (t0) REVERT: E 41 TYR cc_start: 0.8871 (m-80) cc_final: 0.8319 (m-80) REVERT: E 50 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7012 (pt0) REVERT: F 84 MET cc_start: 0.8188 (tpp) cc_final: 0.7918 (mmm) REVERT: G 74 LYS cc_start: 0.7965 (tppt) cc_final: 0.7608 (mmmm) REVERT: H 54 LYS cc_start: 0.8627 (tppt) cc_final: 0.8386 (mmmt) REVERT: K 674 ARG cc_start: 0.8038 (ttp-110) cc_final: 0.7731 (ttp-110) REVERT: K 714 LYS cc_start: 0.8092 (mmtp) cc_final: 0.7796 (mtmm) REVERT: K 763 THR cc_start: 0.7887 (m) cc_final: 0.7471 (p) REVERT: K 841 MET cc_start: 0.5124 (ptt) cc_final: 0.4711 (ptt) REVERT: K 927 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8522 (p) REVERT: K 957 VAL cc_start: 0.8888 (t) cc_final: 0.8638 (t) REVERT: K 1129 ILE cc_start: 0.6719 (OUTLIER) cc_final: 0.6499 (mm) REVERT: L 336 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7737 (mttt) REVERT: L 352 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8418 (mttp) REVERT: M 310 LEU cc_start: 0.8597 (mt) cc_final: 0.8348 (mt) REVERT: M 313 SER cc_start: 0.8884 (p) cc_final: 0.8609 (p) REVERT: M 358 GLN cc_start: 0.8032 (mm110) cc_final: 0.7778 (mm110) REVERT: M 395 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: N 107 LYS cc_start: 0.8348 (mmtp) cc_final: 0.8005 (ttpt) REVERT: N 126 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7117 (pm20) REVERT: N 271 SER cc_start: 0.8767 (t) cc_final: 0.8544 (m) REVERT: N 393 GLN cc_start: 0.8052 (mt0) cc_final: 0.7506 (mp10) REVERT: N 515 GLN cc_start: 0.8353 (mt0) cc_final: 0.7740 (pp30) REVERT: P 538 LYS cc_start: 0.8593 (ptpt) cc_final: 0.8363 (pttt) outliers start: 49 outliers final: 31 residues processed: 357 average time/residue: 0.1607 time to fit residues: 86.4480 Evaluate side-chains 352 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 313 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER 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 49 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 115 LEU Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 927 SER Chi-restraints excluded: chain K residue 973 SER Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1129 ILE Chi-restraints excluded: chain K residue 1134 SER Chi-restraints excluded: chain K residue 1250 VAL 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 155 SER Chi-restraints excluded: chain L residue 160 PHE 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 343 SER Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 126 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 Chi-restraints excluded: chain P residue 545 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 217 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.0980 chunk 224 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN M 275 GLN M 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.184278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130785 restraints weight = 31869.586| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.00 r_work: 0.3365 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27503 Z= 0.134 Angle : 0.527 9.689 38570 Z= 0.299 Chirality : 0.037 0.200 4262 Planarity : 0.004 0.053 3721 Dihedral : 26.380 178.891 6332 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.90 % Allowed : 20.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.18), residues: 2335 helix: 1.78 (0.15), residues: 1298 sheet: -0.19 (0.50), residues: 108 loop : -0.15 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 88 TYR 0.023 0.001 TYR K 726 PHE 0.019 0.001 PHE K1305 TRP 0.006 0.001 TRP K1151 HIS 0.003 0.001 HIS K 998 Details of bonding type rmsd covalent geometry : bond 0.00298 (27486) covalent geometry : angle 0.52504 (38555) hydrogen bonds : bond 0.03316 ( 1394) hydrogen bonds : angle 3.31938 ( 3678) metal coordination : bond 0.00664 ( 17) metal coordination : angle 2.62251 ( 15) ********************** 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 365 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 325 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8564 (p) REVERT: A 129 ARG cc_start: 0.8277 (tpt90) cc_final: 0.8048 (tpt-90) REVERT: B 31 LYS cc_start: 0.8498 (tttt) cc_final: 0.8144 (tttt) REVERT: B 35 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.8061 (mtp-110) REVERT: C 73 ASN cc_start: 0.8266 (t0) cc_final: 0.7822 (t0) REVERT: E 41 TYR cc_start: 0.8772 (m-80) cc_final: 0.8063 (m-80) REVERT: E 42 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7585 (mtt90) REVERT: E 50 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6994 (pt0) REVERT: E 79 LYS cc_start: 0.8297 (tttp) cc_final: 0.7929 (tttp) REVERT: F 27 GLN cc_start: 0.8602 (mp10) cc_final: 0.8034 (mp10) REVERT: F 64 ASN cc_start: 0.8041 (m-40) cc_final: 0.7833 (m110) REVERT: F 84 MET cc_start: 0.7945 (tpp) cc_final: 0.7655 (mmm) REVERT: G 74 LYS cc_start: 0.7860 (tppt) cc_final: 0.7526 (mmmm) REVERT: H 54 LYS cc_start: 0.8568 (tppt) cc_final: 0.8355 (mmmt) REVERT: K 674 ARG cc_start: 0.8079 (ttp-110) cc_final: 0.7861 (ptp-110) REVERT: K 714 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7720 (mtmm) REVERT: K 763 THR cc_start: 0.7719 (m) cc_final: 0.7264 (p) REVERT: K 841 MET cc_start: 0.4828 (ptt) cc_final: 0.4517 (ptt) REVERT: K 927 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8609 (p) REVERT: K 957 VAL cc_start: 0.8804 (t) cc_final: 0.8546 (t) REVERT: K 1208 LEU cc_start: 0.6467 (mt) cc_final: 0.5535 (mp) REVERT: L 88 ARG cc_start: 0.8526 (mtp85) cc_final: 0.8234 (mtp180) REVERT: L 105 ASN cc_start: 0.8620 (t0) cc_final: 0.8216 (t0) REVERT: L 336 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7632 (mttt) REVERT: M 310 LEU cc_start: 0.8452 (mt) cc_final: 0.8183 (mt) REVERT: M 313 SER cc_start: 0.8792 (p) cc_final: 0.8510 (p) REVERT: M 358 GLN cc_start: 0.7985 (mm110) cc_final: 0.7687 (mm110) REVERT: M 395 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: N 107 LYS cc_start: 0.8298 (mmtp) cc_final: 0.7878 (ttpt) REVERT: N 271 SER cc_start: 0.8757 (t) cc_final: 0.8525 (m) REVERT: N 393 GLN cc_start: 0.7940 (mt0) cc_final: 0.7336 (mp10) REVERT: N 515 GLN cc_start: 0.8418 (mt0) cc_final: 0.7705 (pp30) REVERT: P 538 LYS cc_start: 0.8513 (ptpt) cc_final: 0.8278 (pttt) REVERT: P 556 TYR cc_start: 0.6524 (m-10) cc_final: 0.6270 (m-10) outliers start: 40 outliers final: 29 residues processed: 350 average time/residue: 0.1820 time to fit residues: 96.1412 Evaluate side-chains 357 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 323 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER 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 101 THR Chi-restraints excluded: chain D residue 31 LYS 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 115 LEU Chi-restraints excluded: chain K residue 818 ASP Chi-restraints excluded: chain K residue 927 SER Chi-restraints excluded: chain K residue 973 SER Chi-restraints excluded: chain K residue 1134 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 123 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 160 PHE 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 343 SER Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 104 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 216 optimal weight: 8.9990 chunk 252 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 212 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.183849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130316 restraints weight = 31862.880| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.03 r_work: 0.3348 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27503 Z= 0.139 Angle : 0.530 9.000 38570 Z= 0.300 Chirality : 0.037 0.191 4262 Planarity : 0.004 0.052 3721 Dihedral : 26.402 178.699 6332 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.81 % Allowed : 20.17 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.18), residues: 2335 helix: 1.79 (0.15), residues: 1298 sheet: -0.18 (0.50), residues: 108 loop : -0.12 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 88 TYR 0.023 0.001 TYR K 726 PHE 0.020 0.001 PHE K1022 TRP 0.008 0.001 TRP K1151 HIS 0.003 0.001 HIS K 998 Details of bonding type rmsd covalent geometry : bond 0.00313 (27486) covalent geometry : angle 0.52737 (38555) hydrogen bonds : bond 0.03342 ( 1394) hydrogen bonds : angle 3.32037 ( 3678) metal coordination : bond 0.00758 ( 17) metal coordination : angle 2.70520 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7440.51 seconds wall clock time: 127 minutes 26.02 seconds (7646.02 seconds total)