Starting phenix.real_space_refine on Sun Jun 22 12:39:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxy_35082/06_2025/8hxy_35082.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxy_35082/06_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_35082/06_2025/8hxy_35082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxy_35082/06_2025/8hxy_35082.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxy_35082/06_2025/8hxy_35082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxy_35082/06_2025/8hxy_35082.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 340 5.49 5 S 84 5.16 5 C 15578 2.51 5 N 4681 2.21 5 O 5575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26263 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 837 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3466 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "J" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3504 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "K" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4597 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 12, 'TRANS': 536} Chain breaks: 2 Chain: "L" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3048 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 365} Chain: "M" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2398 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Chain: "N" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2769 Classifications: {'peptide': 340} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 319} Chain breaks: 3 Chain: "P" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 272 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23908 SG CYS N 263 75.494 93.776 66.840 1.00 58.89 S ATOM 23925 SG CYS N 266 74.616 91.077 64.280 1.00 62.13 S ATOM 24078 SG CYS N 286 77.192 93.761 63.351 1.00 45.24 S ATOM 23989 SG CYS N 275 76.508 103.330 74.553 1.00 85.58 S ATOM 24010 SG CYS N 278 72.529 103.314 74.084 1.00 90.86 S ATOM 24213 SG CYS N 303 74.840 104.681 71.437 1.00 88.55 S ATOM 24236 SG CYS N 306 74.443 106.489 74.678 1.00 98.42 S ATOM 25138 SG CYS N 417 61.690 54.244 42.378 1.00 30.71 S ATOM 25165 SG CYS N 420 61.658 50.519 41.569 1.00 35.54 S ATOM 25421 SG CYS N 451 64.910 52.529 41.271 1.00 46.29 S ATOM 25326 SG CYS N 440 60.466 66.139 44.417 1.00 42.65 S ATOM 25352 SG CYS N 443 57.546 65.738 41.810 1.00 20.36 S ATOM 25541 SG CYS N 466 61.077 64.437 40.876 1.00 59.47 S Time building chain proxies: 13.34, per 1000 atoms: 0.51 Number of scatterers: 26263 At special positions: 0 Unit cell: (139.65, 158.55, 174.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 84 16.00 P 340 15.00 O 5575 8.00 N 4681 7.00 C 15578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.67 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 501 " pdb="ZN ZN L 501 " - pdb=" ND1 HIS L 188 " pdb=" ZN N 701 " pdb="ZN ZN N 701 " - pdb=" ND1 HIS N 283 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 266 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 263 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 286 " pdb=" ZN N 702 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 303 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 306 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 278 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 275 " pdb=" ZN N 703 " pdb="ZN ZN N 703 " - pdb=" ND1 HIS N 448 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 417 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 451 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 420 " pdb=" ZN N 704 " pdb="ZN ZN N 704 " - pdb=" NE2 HIS N 469 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 443 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 466 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 440 " Number of angles added : 15 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4502 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 19 sheets defined 57.1% alpha, 6.5% beta 168 base pairs and 299 stacking pairs defined. Time for finding SS restraints: 10.90 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: 15.60 Time building geometry restraints manager: 7.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4385 1.32 - 1.45: 8652 1.45 - 1.57: 13637 1.57 - 1.69: 679 1.69 - 1.81: 133 Bond restraints: 27486 Sorted by residual: bond pdb=" CA ARG L 44 " pdb=" C ARG L 44 " ideal model delta sigma weight residual 1.522 1.449 0.073 1.37e-02 5.33e+03 2.83e+01 bond pdb=" CA ARG D 96 " pdb=" C ARG D 96 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.29e-02 6.01e+03 2.24e+01 bond pdb=" CA LEU A 82 " pdb=" C LEU A 82 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.26e-02 6.30e+03 2.11e+01 bond pdb=" CA LYS F 79 " pdb=" C LYS F 79 " ideal model delta sigma weight residual 1.521 1.465 0.056 1.27e-02 6.20e+03 1.93e+01 bond pdb=" CA ASP N 261 " pdb=" C ASP N 261 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.31e-02 5.83e+03 1.92e+01 ... (remaining 27481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 38151 3.66 - 7.31: 368 7.31 - 10.97: 30 10.97 - 14.62: 4 14.62 - 18.28: 2 Bond angle restraints: 38555 Sorted by residual: angle pdb=" N ILE B 50 " pdb=" CA ILE B 50 " pdb=" C ILE B 50 " ideal model delta sigma weight residual 112.12 104.02 8.10 8.40e-01 1.42e+00 9.30e+01 angle pdb=" N GLU A 133 " pdb=" CA GLU A 133 " pdb=" C GLU A 133 " ideal model delta sigma weight residual 113.97 101.71 12.26 1.28e+00 6.10e-01 9.18e+01 angle pdb=" N HIS F 75 " pdb=" CA HIS F 75 " pdb=" C HIS F 75 " ideal model delta sigma weight residual 113.97 104.30 9.67 1.28e+00 6.10e-01 5.71e+01 angle pdb=" N GLY B 48 " pdb=" CA GLY B 48 " pdb=" C GLY B 48 " ideal model delta sigma weight residual 112.51 100.95 11.56 1.53e+00 4.27e-01 5.71e+01 angle pdb=" N HIS M 18 " pdb=" CA HIS M 18 " pdb=" C HIS M 18 " ideal model delta sigma weight residual 110.80 96.06 14.74 2.13e+00 2.20e-01 4.79e+01 ... (remaining 38550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 13846 35.95 - 71.89: 1821 71.89 - 107.84: 21 107.84 - 143.79: 1 143.79 - 179.73: 4 Dihedral angle restraints: 15693 sinusoidal: 8723 harmonic: 6970 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA VAL K 923 " pdb=" C VAL K 923 " pdb=" N PHE K 924 " pdb=" CA PHE K 924 " ideal model delta harmonic sigma weight residual -180.00 -157.78 -22.22 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 15690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3449 0.055 - 0.111: 689 0.111 - 0.166: 102 0.166 - 0.221: 17 0.221 - 0.277: 5 Chirality restraints: 4262 Sorted by residual: chirality pdb=" CB VAL L 363 " pdb=" CA VAL L 363 " pdb=" CG1 VAL L 363 " pdb=" CG2 VAL L 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB THR D 112 " pdb=" CA THR D 112 " pdb=" OG1 THR D 112 " pdb=" CG2 THR D 112 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA GLU E 50 " pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CB GLU E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 4259 not shown) Planarity restraints: 3721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU N 507 " 0.102 5.00e-02 4.00e+02 1.49e-01 3.55e+01 pdb=" N PRO N 508 " -0.257 5.00e-02 4.00e+02 pdb=" CA PRO N 508 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO N 508 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 101 " -0.026 2.00e-02 2.50e+03 5.19e-02 2.70e+01 pdb=" C VAL A 101 " 0.090 2.00e-02 2.50e+03 pdb=" O VAL A 101 " -0.033 2.00e-02 2.50e+03 pdb=" N ALA A 102 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 72 " -0.024 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C ARG A 72 " 0.088 2.00e-02 2.50e+03 pdb=" O ARG A 72 " -0.034 2.00e-02 2.50e+03 pdb=" N GLU A 73 " -0.030 2.00e-02 2.50e+03 ... (remaining 3718 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 727 2.65 - 3.21: 23206 3.21 - 3.78: 48121 3.78 - 4.34: 63316 4.34 - 4.90: 93461 Nonbonded interactions: 228831 Sorted by model distance: nonbonded pdb=" OD1 ASP L 186 " pdb="ZN ZN L 501 " model vdw 2.090 2.230 nonbonded pdb=" OD2 ASP L 274 " pdb="ZN ZN L 501 " model vdw 2.208 2.230 nonbonded pdb=" O ASN K 663 " pdb=" OG1 THR K 667 " model vdw 2.209 3.040 nonbonded pdb=" NH2 ARG B 35 " pdb=" OH TYR B 51 " model vdw 2.220 3.120 nonbonded pdb=" O ARG K1308 " pdb=" OG1 THR K1309 " model vdw 2.260 3.040 ... (remaining 228826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 34 or resid 37 through 134)) selection = (chain 'E' and (resid 12 through 13 or resid 18 or resid 38 through 134)) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = (chain 'H' and resid 29 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 73.820 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 27503 Z= 0.453 Angle : 0.943 18.278 38570 Z= 0.598 Chirality : 0.047 0.277 4262 Planarity : 0.007 0.149 3721 Dihedral : 23.635 179.735 11191 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.10 % Allowed : 15.84 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.16), residues: 2335 helix: -1.21 (0.13), residues: 1222 sheet: -0.37 (0.47), residues: 122 loop : -1.16 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K1223 HIS 0.008 0.001 HIS N 469 PHE 0.039 0.002 PHE N 311 TYR 0.033 0.002 TYR A 99 ARG 0.012 0.001 ARG N 369 Details of bonding type rmsd hydrogen bonds : bond 0.15642 ( 1394) hydrogen bonds : angle 6.63483 ( 3678) metal coordination : bond 0.00768 ( 17) metal coordination : angle 3.24015 ( 15) covalent geometry : bond 0.00679 (27486) covalent geometry : angle 0.94094 (38555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 579 time to evaluate : 2.452 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: 0.4808 time to fit residues: 413.2614 Evaluate side-chains 376 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 260 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 107 optimal weight: 50.0000 chunk 208 optimal weight: 50.0000 chunk 80 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN A 76 GLN C 73 ASN C 112 GLN D 92 GLN E 19 GLN E 39 HIS E 68 GLN E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 73 ASN H 106 HIS K 961 ASN K1311 HIS ** L 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 GLN N 130 ASN N 430 HIS P 541 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.188885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137105 restraints weight = 32003.539| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.83 r_work: 0.3446 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27503 Z= 0.182 Angle : 0.590 8.238 38570 Z= 0.333 Chirality : 0.039 0.190 4262 Planarity : 0.005 0.086 3721 Dihedral : 26.945 176.587 6335 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.66 % Allowed : 17.51 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2335 helix: 0.30 (0.14), residues: 1280 sheet: -0.39 (0.48), residues: 122 loop : -0.68 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K1151 HIS 0.006 0.001 HIS K 930 PHE 0.016 0.002 PHE K 668 TYR 0.031 0.002 TYR H 80 ARG 0.006 0.001 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 1394) hydrogen bonds : angle 3.87292 ( 3678) metal coordination : bond 0.00875 ( 17) metal coordination : angle 3.50422 ( 15) covalent geometry : bond 0.00414 (27486) covalent geometry : angle 0.58650 (38555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 399 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8433 (tp) cc_final: 0.8097 (tp) REVERT: A 90 MET cc_start: 0.8540 (tpp) cc_final: 0.8070 (tpp) REVERT: A 129 ARG cc_start: 0.8429 (tpt90) cc_final: 0.7932 (tpt90) REVERT: B 31 LYS cc_start: 0.8576 (tttt) cc_final: 0.8355 (tttt) REVERT: B 35 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8165 (mmm-85) REVERT: B 93 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7479 (mp10) REVERT: C 35 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7728 (mtm-85) REVERT: C 73 ASN cc_start: 0.8360 (t0) cc_final: 0.7915 (t0) REVERT: D 65 ASP cc_start: 0.8760 (t0) cc_final: 0.8515 (t0) REVERT: D 81 ASN cc_start: 0.8645 (m110) cc_final: 0.8306 (m110) REVERT: E 112 ILE cc_start: 0.9307 (mm) cc_final: 0.9097 (mt) REVERT: F 74 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: F 79 LYS cc_start: 0.8249 (mttp) cc_final: 0.7903 (mmtm) REVERT: H 54 LYS cc_start: 0.8402 (tppt) cc_final: 0.8129 (mmmt) REVERT: H 90 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: H 110 GLU cc_start: 0.8277 (tp30) cc_final: 0.7966 (tp30) REVERT: K 695 ASP cc_start: 0.7891 (m-30) cc_final: 0.7643 (t0) REVERT: K 714 LYS cc_start: 0.8027 (mmtp) cc_final: 0.7787 (mtmm) REVERT: K 764 PHE cc_start: 0.7560 (m-10) cc_final: 0.6995 (m-10) REVERT: K 812 GLU cc_start: 0.7840 (tp30) cc_final: 0.7555 (tp30) REVERT: K 903 GLU cc_start: 0.7764 (pp20) cc_final: 0.7522 (pt0) REVERT: K 957 VAL cc_start: 0.8959 (t) cc_final: 0.8627 (t) REVERT: K 958 ASP cc_start: 0.7875 (m-30) cc_final: 0.7647 (m-30) REVERT: K 1287 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7745 (ttp80) REVERT: L 53 MET cc_start: 0.8747 (mmp) cc_final: 0.8490 (mmm) REVERT: L 61 MET cc_start: 0.8160 (ptp) cc_final: 0.7900 (ptp) REVERT: L 72 GLN cc_start: 0.8269 (tt0) cc_final: 0.7875 (tt0) REVERT: L 105 ASN cc_start: 0.8598 (t0) cc_final: 0.8323 (t0) REVERT: L 248 ARG cc_start: 0.8108 (ttt180) cc_final: 0.7865 (ttt-90) REVERT: M 296 MET cc_start: 0.8006 (ppp) cc_final: 0.7383 (ppp) REVERT: M 395 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: N 107 LYS cc_start: 0.8379 (mmtp) cc_final: 0.8173 (ttpt) REVERT: N 117 LYS cc_start: 0.8233 (mmtp) cc_final: 0.7891 (mmmt) REVERT: N 261 ASP cc_start: 0.8473 (m-30) cc_final: 0.8238 (m-30) REVERT: N 291 ILE cc_start: 0.8131 (mm) cc_final: 0.7878 (mt) REVERT: N 375 GLU cc_start: 0.8329 (pt0) cc_final: 0.8058 (pm20) REVERT: N 496 ARG cc_start: 0.8032 (mtt-85) cc_final: 0.7724 (mtp85) REVERT: N 505 TYR cc_start: 0.7863 (m-80) cc_final: 0.7539 (m-80) REVERT: N 517 ASN cc_start: 0.7129 (t0) cc_final: 0.6923 (t0) outliers start: 56 outliers final: 21 residues processed: 438 average time/residue: 0.4256 time to fit residues: 279.8537 Evaluate side-chains 365 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 341 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 857 HIS Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1179 THR Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 452 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 28 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 194 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 91 optimal weight: 60.0000 chunk 78 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 68 GLN E 93 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.178867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.123843 restraints weight = 31569.602| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.02 r_work: 0.3267 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 27503 Z= 0.240 Angle : 0.619 7.659 38570 Z= 0.347 Chirality : 0.041 0.169 4262 Planarity : 0.005 0.072 3721 Dihedral : 27.097 177.421 6332 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.24 % Allowed : 17.17 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2335 helix: 0.76 (0.14), residues: 1289 sheet: -0.32 (0.48), residues: 121 loop : -0.58 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K1151 HIS 0.005 0.001 HIS L 38 PHE 0.017 0.002 PHE E 67 TYR 0.038 0.002 TYR A 54 ARG 0.006 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 1394) hydrogen bonds : angle 3.77334 ( 3678) metal coordination : bond 0.01352 ( 17) metal coordination : angle 3.53113 ( 15) covalent geometry : bond 0.00559 (27486) covalent geometry : angle 0.61511 (38555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 364 time to evaluate : 2.771 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.8025 (t-90) cc_final: 0.7811 (t-90) REVERT: A 90 MET cc_start: 0.8351 (tpp) cc_final: 0.7688 (tpp) REVERT: A 94 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: B 91 LYS cc_start: 0.8525 (tttp) cc_final: 0.8140 (mtpp) REVERT: B 93 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7287 (mp10) REVERT: C 73 ASN cc_start: 0.8261 (t0) cc_final: 0.7705 (t0) REVERT: D 31 LYS cc_start: 0.8355 (mttt) cc_final: 0.8052 (pttt) REVERT: D 65 ASP cc_start: 0.8944 (t0) cc_final: 0.8705 (t0) REVERT: E 41 TYR cc_start: 0.8911 (m-80) cc_final: 0.8687 (m-80) REVERT: E 50 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7225 (pt0) REVERT: F 79 LYS cc_start: 0.8378 (mttp) cc_final: 0.7963 (mmtm) REVERT: F 84 MET cc_start: 0.8262 (tpp) cc_final: 0.7905 (mmm) REVERT: G 74 LYS cc_start: 0.7726 (tppt) cc_final: 0.7366 (mmmm) REVERT: H 54 LYS cc_start: 0.8671 (tppt) cc_final: 0.8451 (mmmt) REVERT: H 110 GLU cc_start: 0.8588 (tp30) cc_final: 0.8381 (tp30) REVERT: H 117 LYS cc_start: 0.8337 (tttt) cc_final: 0.8114 (tttm) REVERT: K 668 PHE cc_start: 0.7778 (t80) cc_final: 0.7424 (t80) REVERT: K 694 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7999 (mm-40) REVERT: K 860 MET cc_start: 0.8447 (tpp) cc_final: 0.8215 (mmm) REVERT: K 957 VAL cc_start: 0.8856 (t) cc_final: 0.8592 (t) REVERT: K 1268 LEU cc_start: 0.8730 (mt) cc_final: 0.8385 (mt) REVERT: L 53 MET cc_start: 0.8939 (mmp) cc_final: 0.8620 (mmm) REVERT: L 61 MET cc_start: 0.8286 (ptp) cc_final: 0.7967 (ptp) REVERT: L 72 GLN cc_start: 0.8598 (tt0) cc_final: 0.8053 (tt0) REVERT: L 105 ASN cc_start: 0.8663 (t0) cc_final: 0.8418 (t0) REVERT: M 242 ASP cc_start: 0.8377 (m-30) cc_final: 0.7967 (m-30) REVERT: M 280 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: M 310 LEU cc_start: 0.8442 (mt) cc_final: 0.8123 (mt) REVERT: M 395 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: N 107 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8165 (ttpt) REVERT: N 260 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7592 (mt-10) REVERT: N 261 ASP cc_start: 0.8538 (m-30) cc_final: 0.8250 (m-30) REVERT: N 271 SER cc_start: 0.8811 (t) cc_final: 0.8499 (m) REVERT: N 331 ASN cc_start: 0.6527 (t0) cc_final: 0.6178 (t0) REVERT: N 393 GLN cc_start: 0.8248 (mt0) cc_final: 0.7456 (mp10) REVERT: N 395 ILE cc_start: 0.8802 (tp) cc_final: 0.8557 (tp) outliers start: 68 outliers final: 39 residues processed: 410 average time/residue: 0.4901 time to fit residues: 303.3056 Evaluate side-chains 368 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 325 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1295 SER Chi-restraints excluded: chain K residue 1297 THR Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 265 SER Chi-restraints excluded: chain L residue 350 ASP Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 365 THR Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 325 ILE 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 449 LEU Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 190 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 234 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 216 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 293 ASN ** 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 = 0.4197 r_free = 0.4197 target = 0.185455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.132746 restraints weight = 32042.968| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.90 r_work: 0.3395 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3456 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= 0.148 Angle : 0.537 9.956 38570 Z= 0.306 Chirality : 0.037 0.156 4262 Planarity : 0.004 0.058 3721 Dihedral : 26.768 177.942 6332 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.28 % Allowed : 18.55 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2335 helix: 1.19 (0.15), residues: 1285 sheet: -0.39 (0.48), residues: 122 loop : -0.40 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1151 HIS 0.003 0.001 HIS H 46 PHE 0.013 0.001 PHE E 67 TYR 0.030 0.001 TYR A 54 ARG 0.007 0.000 ARG L 88 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 1394) hydrogen bonds : angle 3.52911 ( 3678) metal coordination : bond 0.00762 ( 17) metal coordination : angle 2.97555 ( 15) covalent geometry : bond 0.00333 (27486) covalent geometry : angle 0.53427 (38555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 347 time to evaluate : 3.053 Fit side-chains revert: symmetry clash REVERT: A 87 SER cc_start: 0.8863 (m) cc_final: 0.8476 (p) REVERT: A 90 MET cc_start: 0.8265 (tpp) cc_final: 0.7478 (tpp) REVERT: A 94 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: B 91 LYS cc_start: 0.8605 (tttp) cc_final: 0.8178 (mtpp) REVERT: B 93 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7496 (mm110) REVERT: C 73 ASN cc_start: 0.8413 (t0) cc_final: 0.7921 (t0) REVERT: D 31 LYS cc_start: 0.8324 (mttt) cc_final: 0.8096 (pttt) REVERT: D 65 ASP cc_start: 0.8793 (t0) cc_final: 0.8330 (t0) REVERT: E 41 TYR cc_start: 0.8910 (m-80) cc_final: 0.8676 (m-80) REVERT: E 79 LYS cc_start: 0.8419 (tttp) cc_final: 0.7947 (tttp) REVERT: F 79 LYS cc_start: 0.8221 (mttp) cc_final: 0.7908 (mmtm) REVERT: F 84 MET cc_start: 0.8246 (tpp) cc_final: 0.7979 (mmm) REVERT: G 74 LYS cc_start: 0.7830 (tppt) cc_final: 0.7502 (mmmm) REVERT: H 54 LYS cc_start: 0.8642 (tppt) cc_final: 0.8388 (mmmt) REVERT: H 65 ASP cc_start: 0.8236 (t70) cc_final: 0.8011 (t0) REVERT: K 668 PHE cc_start: 0.7834 (t80) cc_final: 0.7414 (t80) REVERT: K 763 THR cc_start: 0.7862 (m) cc_final: 0.7485 (p) REVERT: K 841 MET cc_start: 0.5438 (ptt) cc_final: 0.4973 (ptt) REVERT: K 860 MET cc_start: 0.8496 (tpp) cc_final: 0.8252 (mmm) REVERT: K 957 VAL cc_start: 0.8846 (t) cc_final: 0.8576 (t) REVERT: K 1268 LEU cc_start: 0.8710 (mt) cc_final: 0.8389 (mt) REVERT: L 61 MET cc_start: 0.8136 (ptp) cc_final: 0.7835 (ptp) REVERT: L 88 ARG cc_start: 0.8345 (mtp85) cc_final: 0.8008 (mtp180) REVERT: L 105 ASN cc_start: 0.8563 (t0) cc_final: 0.8358 (t0) REVERT: L 133 ARG cc_start: 0.8575 (mtp85) cc_final: 0.8298 (mtp85) REVERT: M 280 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: M 395 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: N 107 LYS cc_start: 0.8504 (mmtp) cc_final: 0.8124 (ttpt) REVERT: N 260 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7569 (mt-10) REVERT: N 271 SER cc_start: 0.8816 (t) cc_final: 0.8549 (m) REVERT: N 331 ASN cc_start: 0.6266 (t0) cc_final: 0.5875 (t0) REVERT: N 344 ASP cc_start: 0.7911 (m-30) cc_final: 0.7540 (m-30) REVERT: N 393 GLN cc_start: 0.8226 (mt0) cc_final: 0.7621 (mp10) REVERT: P 537 PHE cc_start: 0.8377 (m-10) cc_final: 0.8164 (m-10) REVERT: P 538 LYS cc_start: 0.8562 (ptpt) cc_final: 0.8247 (pttt) outliers start: 48 outliers final: 31 residues processed: 377 average time/residue: 0.4924 time to fit residues: 278.3493 Evaluate side-chains 349 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 315 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 772 ASP Chi-restraints excluded: chain K residue 857 HIS Chi-restraints excluded: chain K residue 858 THR Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 296 MET 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 449 LEU 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 1 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 227 optimal weight: 0.4980 chunk 197 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 chunk 224 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 chunk 205 optimal weight: 50.0000 chunk 145 optimal weight: 0.6980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN F 64 ASN G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1165 ASN ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 535 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.177359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122284 restraints weight = 31756.809| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.96 r_work: 0.3252 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 27503 Z= 0.235 Angle : 0.606 11.011 38570 Z= 0.339 Chirality : 0.040 0.184 4262 Planarity : 0.005 0.053 3721 Dihedral : 27.005 177.175 6332 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.38 % Allowed : 18.08 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2335 helix: 1.01 (0.14), residues: 1300 sheet: -0.53 (0.50), residues: 105 loop : -0.47 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K1151 HIS 0.005 0.001 HIS L 38 PHE 0.017 0.002 PHE K 723 TYR 0.034 0.002 TYR A 54 ARG 0.010 0.001 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 1394) hydrogen bonds : angle 3.64786 ( 3678) metal coordination : bond 0.01534 ( 17) metal coordination : angle 3.53765 ( 15) covalent geometry : bond 0.00552 (27486) covalent geometry : angle 0.60207 (38555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 335 time to evaluate : 2.556 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8321 (tpp) cc_final: 0.7594 (tpp) REVERT: A 94 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: B 35 ARG cc_start: 0.8350 (ttm110) cc_final: 0.7948 (mmm-85) REVERT: B 91 LYS cc_start: 0.8552 (tttp) cc_final: 0.8043 (tttm) REVERT: B 93 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7545 (mm110) REVERT: C 73 ASN cc_start: 0.8290 (t0) cc_final: 0.7767 (t0) REVERT: D 31 LYS cc_start: 0.8445 (mttt) cc_final: 0.8073 (pttt) REVERT: D 65 ASP cc_start: 0.8947 (t0) cc_final: 0.8716 (t0) REVERT: D 81 ASN cc_start: 0.8821 (m-40) cc_final: 0.8361 (m110) REVERT: E 41 TYR cc_start: 0.8784 (m-80) cc_final: 0.8428 (m-80) REVERT: E 42 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7799 (mtt-85) REVERT: E 50 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7329 (pt0) REVERT: F 79 LYS cc_start: 0.8362 (mttp) cc_final: 0.7942 (mmtm) REVERT: F 84 MET cc_start: 0.8306 (tpp) cc_final: 0.7964 (mmm) REVERT: G 74 LYS cc_start: 0.7887 (tppt) cc_final: 0.7537 (mmmm) REVERT: H 54 LYS cc_start: 0.8677 (tppt) cc_final: 0.8447 (mmmt) REVERT: H 65 ASP cc_start: 0.8297 (t70) cc_final: 0.8018 (t0) REVERT: K 727 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6794 (mp10) REVERT: K 763 THR cc_start: 0.7810 (m) cc_final: 0.7407 (p) REVERT: K 957 VAL cc_start: 0.8850 (t) cc_final: 0.8613 (t) REVERT: K 1268 LEU cc_start: 0.8688 (mt) cc_final: 0.8298 (mt) REVERT: L 53 MET cc_start: 0.8894 (mmt) cc_final: 0.8661 (mmm) REVERT: L 61 MET cc_start: 0.8264 (ptp) cc_final: 0.7929 (ptp) REVERT: L 72 GLN cc_start: 0.8614 (tt0) cc_final: 0.8122 (tt0) REVERT: L 105 ASN cc_start: 0.8698 (t0) cc_final: 0.8408 (t0) REVERT: L 247 TYR cc_start: 0.8442 (t80) cc_final: 0.8158 (t80) REVERT: L 352 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8461 (mttp) REVERT: M 242 ASP cc_start: 0.8317 (m-30) cc_final: 0.7963 (m-30) REVERT: M 280 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7837 (tp30) REVERT: M 395 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: N 107 LYS cc_start: 0.8528 (mmtp) cc_final: 0.7972 (ttpt) REVERT: N 271 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8518 (m) REVERT: N 331 ASN cc_start: 0.6674 (t0) cc_final: 0.6367 (t0) REVERT: N 344 ASP cc_start: 0.8128 (m-30) cc_final: 0.7714 (m-30) REVERT: N 393 GLN cc_start: 0.8210 (mt0) cc_final: 0.7427 (mp10) REVERT: N 515 GLN cc_start: 0.8567 (mt0) cc_final: 0.7609 (pp30) REVERT: P 537 PHE cc_start: 0.8464 (m-10) cc_final: 0.8135 (m-10) REVERT: P 538 LYS cc_start: 0.8589 (ptpt) cc_final: 0.8353 (pttt) outliers start: 71 outliers final: 47 residues processed: 383 average time/residue: 0.4271 time to fit residues: 247.7112 Evaluate side-chains 370 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 317 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 903 GLU Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1165 ASN Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain K residue 1295 SER Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 352 LYS Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 365 THR Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 315 LYS Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 271 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 449 LEU Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 555 ILE Chi-restraints excluded: chain P residue 558 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 203 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 163 optimal weight: 0.5980 chunk 217 optimal weight: 4.9990 chunk 265 optimal weight: 7.9990 chunk 249 optimal weight: 4.9990 chunk 197 optimal weight: 0.7980 chunk 150 optimal weight: 0.0040 chunk 144 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 ASN G 31 HIS G 68 ASN G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1165 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.185354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.133282 restraints weight = 31876.375| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.87 r_work: 0.3407 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3862 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= 0.137 Angle : 0.534 11.127 38570 Z= 0.304 Chirality : 0.037 0.204 4262 Planarity : 0.004 0.053 3721 Dihedral : 26.605 178.723 6332 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.62 % Allowed : 19.08 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.17), residues: 2335 helix: 1.39 (0.15), residues: 1300 sheet: -0.53 (0.51), residues: 106 loop : -0.36 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 301 HIS 0.003 0.001 HIS L 78 PHE 0.013 0.001 PHE L 160 TYR 0.018 0.001 TYR A 54 ARG 0.008 0.000 ARG L 88 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 1394) hydrogen bonds : angle 3.43112 ( 3678) metal coordination : bond 0.00688 ( 17) metal coordination : angle 2.84897 ( 15) covalent geometry : bond 0.00303 (27486) covalent geometry : angle 0.53155 (38555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 334 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8801 (m) cc_final: 0.8463 (p) REVERT: A 90 MET cc_start: 0.8284 (tpp) cc_final: 0.7563 (tpp) REVERT: A 94 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: B 35 ARG cc_start: 0.8325 (ttm110) cc_final: 0.8010 (mmm-85) REVERT: B 93 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7412 (mm110) REVERT: C 73 ASN cc_start: 0.8415 (t0) cc_final: 0.7931 (t0) REVERT: D 31 LYS cc_start: 0.8379 (mttt) cc_final: 0.8093 (pttt) REVERT: D 65 ASP cc_start: 0.8753 (t0) cc_final: 0.8284 (t0) REVERT: E 41 TYR cc_start: 0.8768 (m-80) cc_final: 0.8152 (m-80) REVERT: E 42 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7884 (mtt-85) REVERT: E 50 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6941 (pt0) REVERT: F 79 LYS cc_start: 0.8172 (mttp) cc_final: 0.7858 (mmtm) REVERT: F 84 MET cc_start: 0.8134 (tpp) cc_final: 0.7883 (mmm) REVERT: G 42 ARG cc_start: 0.8325 (mtp-110) cc_final: 0.8084 (mtp85) REVERT: G 95 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8263 (tttm) REVERT: H 54 LYS cc_start: 0.8608 (tppt) cc_final: 0.8382 (mmmt) REVERT: K 668 PHE cc_start: 0.7839 (t80) cc_final: 0.7414 (t80) REVERT: K 727 GLN cc_start: 0.6928 (mm-40) cc_final: 0.6710 (mp10) REVERT: K 841 MET cc_start: 0.5602 (ptt) cc_final: 0.5105 (ptt) REVERT: K 957 VAL cc_start: 0.8847 (t) cc_final: 0.8592 (t) REVERT: K 958 ASP cc_start: 0.7602 (m-30) cc_final: 0.7339 (m-30) REVERT: L 105 ASN cc_start: 0.8543 (t0) cc_final: 0.8313 (t0) REVERT: M 242 ASP cc_start: 0.8191 (m-30) cc_final: 0.7867 (m-30) REVERT: M 280 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: M 395 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: N 107 LYS cc_start: 0.8445 (mmtp) cc_final: 0.8075 (ttpt) REVERT: N 271 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8530 (m) REVERT: N 331 ASN cc_start: 0.6268 (t0) cc_final: 0.5954 (t0) REVERT: N 344 ASP cc_start: 0.7939 (m-30) cc_final: 0.7529 (m-30) REVERT: N 393 GLN cc_start: 0.8219 (mt0) cc_final: 0.7686 (mp10) REVERT: N 515 GLN cc_start: 0.8349 (mt0) cc_final: 0.7482 (pp30) REVERT: P 538 LYS cc_start: 0.8632 (ptpt) cc_final: 0.8365 (pttt) outliers start: 55 outliers final: 36 residues processed: 370 average time/residue: 0.4472 time to fit residues: 249.8351 Evaluate side-chains 358 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 317 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 9 LYS Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 772 ASP Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 858 THR Chi-restraints excluded: chain K residue 973 SER Chi-restraints excluded: chain K residue 1165 ASN Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 271 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 558 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 169 optimal weight: 4.9990 chunk 165 optimal weight: 0.6980 chunk 66 optimal weight: 0.3980 chunk 153 optimal weight: 0.9980 chunk 221 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1150 HIS K1165 ASN L 76 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.186221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134072 restraints weight = 32003.691| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.92 r_work: 0.3420 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3915 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= 0.130 Angle : 0.525 11.842 38570 Z= 0.299 Chirality : 0.036 0.199 4262 Planarity : 0.004 0.052 3721 Dihedral : 26.532 178.581 6332 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.57 % Allowed : 19.27 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 2335 helix: 1.59 (0.15), residues: 1301 sheet: -0.39 (0.51), residues: 106 loop : -0.26 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 31 HIS 0.003 0.001 HIS K 998 PHE 0.022 0.001 PHE K 723 TYR 0.019 0.001 TYR M 373 ARG 0.010 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 1394) hydrogen bonds : angle 3.35037 ( 3678) metal coordination : bond 0.00725 ( 17) metal coordination : angle 2.71490 ( 15) covalent geometry : bond 0.00286 (27486) covalent geometry : angle 0.52247 (38555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 332 time to evaluate : 2.273 Fit side-chains revert: symmetry clash REVERT: A 87 SER cc_start: 0.8809 (m) cc_final: 0.8490 (p) REVERT: A 94 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: B 35 ARG cc_start: 0.8268 (ttm110) cc_final: 0.7974 (mmm-85) REVERT: B 91 LYS cc_start: 0.8649 (tttp) cc_final: 0.8238 (mtpp) REVERT: B 93 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7399 (mm110) REVERT: C 73 ASN cc_start: 0.8465 (t0) cc_final: 0.7934 (t0) REVERT: D 31 LYS cc_start: 0.8382 (mttt) cc_final: 0.8097 (pttt) REVERT: D 65 ASP cc_start: 0.8648 (t0) cc_final: 0.8218 (t0) REVERT: D 90 GLU cc_start: 0.7619 (tt0) cc_final: 0.7329 (tt0) REVERT: E 41 TYR cc_start: 0.8811 (m-80) cc_final: 0.8114 (m-80) REVERT: E 42 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7863 (mtt90) REVERT: E 50 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6938 (pt0) REVERT: F 84 MET cc_start: 0.8130 (tpp) cc_final: 0.7870 (mmm) REVERT: G 42 ARG cc_start: 0.8291 (mtp-110) cc_final: 0.8038 (mtp85) REVERT: G 74 LYS cc_start: 0.7831 (tppt) cc_final: 0.7433 (mmmm) REVERT: G 95 LYS cc_start: 0.8490 (ttmm) cc_final: 0.8264 (tttm) REVERT: H 54 LYS cc_start: 0.8549 (tppt) cc_final: 0.8338 (mmmt) REVERT: H 65 ASP cc_start: 0.8461 (t0) cc_final: 0.8243 (t70) REVERT: K 668 PHE cc_start: 0.7813 (t80) cc_final: 0.7381 (t80) REVERT: K 841 MET cc_start: 0.5544 (ptt) cc_final: 0.5002 (ptt) REVERT: K 957 VAL cc_start: 0.8852 (t) cc_final: 0.8601 (t) REVERT: K 958 ASP cc_start: 0.7642 (m-30) cc_final: 0.7381 (m-30) REVERT: K 1129 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6541 (mm) REVERT: K 1273 ARG cc_start: 0.7258 (tpt-90) cc_final: 0.7030 (tpt-90) REVERT: L 105 ASN cc_start: 0.8547 (t0) cc_final: 0.8309 (t0) REVERT: M 280 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7682 (tp30) REVERT: M 395 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: N 107 LYS cc_start: 0.8347 (mmtp) cc_final: 0.7992 (ttpt) REVERT: N 271 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8504 (m) REVERT: N 331 ASN cc_start: 0.6158 (t0) cc_final: 0.5832 (t0) REVERT: N 344 ASP cc_start: 0.7939 (m-30) cc_final: 0.7528 (m-30) REVERT: N 375 GLU cc_start: 0.8084 (pt0) cc_final: 0.7819 (pm20) REVERT: N 393 GLN cc_start: 0.8010 (mt0) cc_final: 0.7451 (mp10) REVERT: N 515 GLN cc_start: 0.8315 (mt0) cc_final: 0.7693 (pp30) outliers start: 54 outliers final: 37 residues processed: 365 average time/residue: 0.4420 time to fit residues: 243.4510 Evaluate side-chains 354 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 311 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 772 ASP Chi-restraints excluded: chain K residue 777 VAL Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1129 ILE Chi-restraints excluded: chain K residue 1165 ASN Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 160 PHE Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 315 LYS Chi-restraints excluded: chain M residue 395 GLU Chi-restraints excluded: chain N residue 271 SER Chi-restraints excluded: chain N residue 294 ASN Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 555 ILE Chi-restraints excluded: chain P residue 558 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 112 optimal weight: 0.0970 chunk 30 optimal weight: 0.0020 chunk 173 optimal weight: 3.9990 chunk 254 optimal weight: 0.5980 chunk 193 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 229 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 222 optimal weight: 0.0870 chunk 124 optimal weight: 7.9990 overall best weight: 0.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** 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 = 0.4240 r_free = 0.4240 target = 0.189492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.138182 restraints weight = 32062.210| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.86 r_work: 0.3496 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4010 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 11.534 38570 Z= 0.294 Chirality : 0.036 0.218 4262 Planarity : 0.004 0.052 3721 Dihedral : 26.379 178.925 6332 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.00 % Allowed : 19.93 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.18), residues: 2335 helix: 1.77 (0.15), residues: 1300 sheet: -0.28 (0.51), residues: 106 loop : -0.19 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 31 HIS 0.003 0.001 HIS K 998 PHE 0.015 0.001 PHE L 160 TYR 0.012 0.001 TYR H 37 ARG 0.010 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 1394) hydrogen bonds : angle 3.26684 ( 3678) metal coordination : bond 0.00662 ( 17) metal coordination : angle 2.61650 ( 15) covalent geometry : bond 0.00263 (27486) covalent geometry : angle 0.51334 (38555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 330 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8763 (m) cc_final: 0.8442 (p) REVERT: A 94 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: B 35 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7950 (mmm-85) REVERT: B 91 LYS cc_start: 0.8629 (tttp) cc_final: 0.8238 (mtpp) REVERT: C 73 ASN cc_start: 0.8366 (t0) cc_final: 0.7889 (t0) REVERT: D 31 LYS cc_start: 0.8362 (mttt) cc_final: 0.8114 (pttt) REVERT: E 41 TYR cc_start: 0.8812 (m-80) cc_final: 0.8284 (m-80) REVERT: E 50 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6845 (pt0) REVERT: E 115 LYS cc_start: 0.9009 (mptt) cc_final: 0.8790 (mmtm) REVERT: F 77 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8150 (mmtm) REVERT: F 84 MET cc_start: 0.7997 (tpp) cc_final: 0.7767 (mmm) REVERT: G 42 ARG cc_start: 0.8341 (mtp-110) cc_final: 0.8008 (mtp85) REVERT: G 74 LYS cc_start: 0.7757 (tppt) cc_final: 0.7395 (mmmm) REVERT: G 95 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8303 (tttm) REVERT: H 54 LYS cc_start: 0.8559 (tppt) cc_final: 0.8346 (mmmt) REVERT: K 668 PHE cc_start: 0.7768 (t80) cc_final: 0.7372 (t80) REVERT: K 714 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7719 (mtmm) REVERT: K 841 MET cc_start: 0.5201 (ptt) cc_final: 0.4723 (ptt) REVERT: K 860 MET cc_start: 0.8419 (tpp) cc_final: 0.8207 (mmm) REVERT: K 918 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8308 (mm-30) REVERT: K 957 VAL cc_start: 0.8911 (t) cc_final: 0.8705 (t) REVERT: K 1129 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6463 (mm) REVERT: L 88 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8179 (mtp85) REVERT: L 105 ASN cc_start: 0.8518 (t0) cc_final: 0.8269 (t0) REVERT: M 280 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7556 (tp30) REVERT: N 107 LYS cc_start: 0.8348 (mmtp) cc_final: 0.8040 (ttpt) REVERT: N 271 SER cc_start: 0.8730 (t) cc_final: 0.8506 (m) REVERT: N 344 ASP cc_start: 0.7791 (m-30) cc_final: 0.7410 (m-30) REVERT: N 393 GLN cc_start: 0.7902 (mt0) cc_final: 0.7408 (mp10) REVERT: N 506 TYR cc_start: 0.7462 (t80) cc_final: 0.7179 (t80) REVERT: N 515 GLN cc_start: 0.8255 (mt0) cc_final: 0.7703 (pp30) REVERT: P 541 GLN cc_start: 0.8109 (mt0) cc_final: 0.7763 (mm-40) outliers start: 42 outliers final: 31 residues processed: 358 average time/residue: 0.4456 time to fit residues: 238.7792 Evaluate side-chains 343 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 307 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 777 VAL Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 858 THR Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1129 ILE Chi-restraints excluded: chain K residue 1165 ASN Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 88 ARG Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 160 PHE Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 372 GLU Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 338 LYS Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 555 ILE Chi-restraints excluded: chain P residue 558 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 206 optimal weight: 30.0000 chunk 77 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 202 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 236 optimal weight: 7.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.177878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.122695 restraints weight = 31925.146| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.00 r_work: 0.3260 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 27503 Z= 0.242 Angle : 0.619 10.675 38570 Z= 0.343 Chirality : 0.041 0.203 4262 Planarity : 0.005 0.051 3721 Dihedral : 26.856 177.680 6332 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.33 % Allowed : 19.89 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.17), residues: 2335 helix: 1.34 (0.14), residues: 1301 sheet: -0.71 (0.49), residues: 111 loop : -0.30 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K1151 HIS 0.005 0.001 HIS L 38 PHE 0.032 0.002 PHE L 160 TYR 0.025 0.002 TYR A 54 ARG 0.011 0.001 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 1394) hydrogen bonds : angle 3.56551 ( 3678) metal coordination : bond 0.01578 ( 17) metal coordination : angle 3.52954 ( 15) covalent geometry : bond 0.00569 (27486) covalent geometry : angle 0.61485 (38555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 329 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: A 129 ARG cc_start: 0.8376 (tpt90) cc_final: 0.8115 (tpt-90) REVERT: B 91 LYS cc_start: 0.8580 (tttp) cc_final: 0.8065 (tttm) REVERT: C 73 ASN cc_start: 0.8346 (t0) cc_final: 0.7821 (t0) REVERT: D 31 LYS cc_start: 0.8424 (mttt) cc_final: 0.8063 (pttt) REVERT: D 65 ASP cc_start: 0.8901 (t0) cc_final: 0.8439 (t0) REVERT: D 81 ASN cc_start: 0.8785 (m-40) cc_final: 0.8433 (m110) REVERT: E 41 TYR cc_start: 0.8798 (m-80) cc_final: 0.8254 (m-80) REVERT: E 42 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7782 (mtt-85) REVERT: E 50 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7149 (pt0) REVERT: F 77 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8448 (mmtm) REVERT: F 84 MET cc_start: 0.8211 (tpp) cc_final: 0.7880 (mmm) REVERT: G 42 ARG cc_start: 0.8361 (mtp-110) cc_final: 0.8121 (mtp85) REVERT: G 74 LYS cc_start: 0.7851 (tppt) cc_final: 0.7482 (mmmm) REVERT: H 54 LYS cc_start: 0.8667 (tppt) cc_final: 0.8452 (mmmt) REVERT: K 674 ARG cc_start: 0.8078 (ttp-110) cc_final: 0.7765 (ttp-110) REVERT: K 841 MET cc_start: 0.5665 (ptt) cc_final: 0.5046 (ptt) REVERT: K 877 PHE cc_start: 0.7533 (m-80) cc_final: 0.7277 (m-80) REVERT: K 957 VAL cc_start: 0.8859 (t) cc_final: 0.8607 (t) REVERT: K 1129 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6496 (mm) REVERT: L 72 GLN cc_start: 0.8624 (tt0) cc_final: 0.8063 (tt0) REVERT: L 105 ASN cc_start: 0.8685 (t0) cc_final: 0.8425 (t0) REVERT: M 242 ASP cc_start: 0.8338 (m-30) cc_final: 0.8005 (m-30) REVERT: M 264 GLU cc_start: 0.7841 (tt0) cc_final: 0.7570 (tt0) REVERT: M 280 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7849 (tp30) REVERT: M 308 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7415 (mt-10) REVERT: M 340 GLU cc_start: 0.8081 (tp30) cc_final: 0.7750 (tt0) REVERT: M 358 GLN cc_start: 0.8175 (mm110) cc_final: 0.7901 (mm110) REVERT: M 395 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: N 107 LYS cc_start: 0.8383 (mmtp) cc_final: 0.7963 (ttpt) REVERT: N 271 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8560 (m) REVERT: N 331 ASN cc_start: 0.6521 (t0) cc_final: 0.6208 (t0) REVERT: N 344 ASP cc_start: 0.8070 (m-30) cc_final: 0.7656 (m-30) REVERT: N 393 GLN cc_start: 0.8281 (mt0) cc_final: 0.7570 (mp10) REVERT: N 506 TYR cc_start: 0.7479 (t80) cc_final: 0.7148 (t80) REVERT: N 515 GLN cc_start: 0.8558 (mt0) cc_final: 0.7809 (pp30) outliers start: 49 outliers final: 32 residues processed: 359 average time/residue: 0.4196 time to fit residues: 226.8521 Evaluate side-chains 356 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 318 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 1010 LEU Chi-restraints excluded: chain K residue 1129 ILE Chi-restraints excluded: chain K residue 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 160 PHE Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 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 Chi-restraints excluded: chain P residue 555 ILE Chi-restraints excluded: chain P residue 558 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 226 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 207 optimal weight: 50.0000 chunk 230 optimal weight: 8.9990 chunk 211 optimal weight: 0.9990 chunk 195 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 113 optimal weight: 0.1980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN E 108 ASN ** H 81 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.184253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131982 restraints weight = 31835.609| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.89 r_work: 0.3414 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27503 Z= 0.150 Angle : 0.551 10.806 38570 Z= 0.310 Chirality : 0.037 0.206 4262 Planarity : 0.004 0.051 3721 Dihedral : 26.588 178.964 6332 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.05 % Allowed : 20.36 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2335 helix: 1.53 (0.15), residues: 1299 sheet: -0.67 (0.49), residues: 111 loop : -0.21 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K1151 HIS 0.003 0.001 HIS L 38 PHE 0.024 0.001 PHE L 160 TYR 0.017 0.001 TYR A 54 ARG 0.010 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 1394) hydrogen bonds : angle 3.43614 ( 3678) metal coordination : bond 0.00819 ( 17) metal coordination : angle 2.82983 ( 15) covalent geometry : bond 0.00341 (27486) covalent geometry : angle 0.54794 (38555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4670 Ramachandran restraints generated. 2335 Oldfield, 0 Emsley, 2335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 319 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: B 35 ARG cc_start: 0.8331 (ttm110) cc_final: 0.8009 (mmm-85) REVERT: B 91 LYS cc_start: 0.8748 (tttp) cc_final: 0.8299 (tttm) REVERT: C 73 ASN cc_start: 0.8451 (t0) cc_final: 0.7957 (t0) REVERT: D 31 LYS cc_start: 0.8410 (mttt) cc_final: 0.8149 (pttt) REVERT: D 65 ASP cc_start: 0.8776 (t0) cc_final: 0.8412 (t0) REVERT: E 41 TYR cc_start: 0.8936 (m-80) cc_final: 0.8493 (m-80) REVERT: E 42 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7867 (mtt90) REVERT: E 50 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6899 (pt0) REVERT: F 84 MET cc_start: 0.8171 (tpp) cc_final: 0.7930 (mmm) REVERT: G 41 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7673 (mt-10) REVERT: G 42 ARG cc_start: 0.8364 (mtp-110) cc_final: 0.8116 (mtp85) REVERT: G 74 LYS cc_start: 0.7828 (tppt) cc_final: 0.7527 (mmmm) REVERT: G 95 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8281 (tttm) REVERT: H 54 LYS cc_start: 0.8590 (tppt) cc_final: 0.8375 (mmmt) REVERT: K 668 PHE cc_start: 0.7948 (t80) cc_final: 0.7627 (t80) REVERT: K 674 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7700 (ttp-110) REVERT: K 841 MET cc_start: 0.5643 (ptt) cc_final: 0.5034 (ptt) REVERT: K 860 MET cc_start: 0.8541 (tpp) cc_final: 0.8339 (mmm) REVERT: K 957 VAL cc_start: 0.8879 (t) cc_final: 0.8614 (t) REVERT: K 1129 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6519 (mm) REVERT: L 105 ASN cc_start: 0.8525 (t0) cc_final: 0.8306 (t0) REVERT: L 288 MET cc_start: 0.8234 (ttp) cc_final: 0.8007 (mtp) REVERT: M 242 ASP cc_start: 0.8069 (m-30) cc_final: 0.7755 (m-30) REVERT: M 280 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: M 358 GLN cc_start: 0.7986 (mm110) cc_final: 0.7720 (mm110) REVERT: M 395 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: N 107 LYS cc_start: 0.8308 (mmtp) cc_final: 0.8067 (ttpt) REVERT: N 271 SER cc_start: 0.8787 (t) cc_final: 0.8568 (m) REVERT: N 331 ASN cc_start: 0.5991 (t0) cc_final: 0.5662 (t0) REVERT: N 344 ASP cc_start: 0.7845 (m-30) cc_final: 0.7558 (m-30) REVERT: N 375 GLU cc_start: 0.8063 (pt0) cc_final: 0.7795 (pm20) REVERT: N 393 GLN cc_start: 0.8114 (mt0) cc_final: 0.7605 (mp10) REVERT: N 506 TYR cc_start: 0.7530 (t80) cc_final: 0.7300 (t80) REVERT: N 515 GLN cc_start: 0.8413 (mt0) cc_final: 0.7797 (pp30) outliers start: 43 outliers final: 35 residues processed: 343 average time/residue: 0.4358 time to fit residues: 226.0051 Evaluate side-chains 352 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 312 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 812 GLU Chi-restraints excluded: chain K residue 1129 ILE Chi-restraints excluded: chain K residue 1250 VAL Chi-restraints excluded: chain K residue 1266 MET Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 156 GLU Chi-restraints excluded: chain L residue 205 THR Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 296 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 338 LYS Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain P residue 545 ASN Chi-restraints excluded: chain P residue 555 ILE Chi-restraints excluded: chain P residue 558 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 250 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 249 optimal weight: 7.9990 chunk 74 optimal weight: 80.0000 chunk 196 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.183188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130319 restraints weight = 31845.341| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.85 r_work: 0.3398 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27503 Z= 0.169 Angle : 0.559 10.336 38570 Z= 0.314 Chirality : 0.038 0.199 4262 Planarity : 0.004 0.051 3721 Dihedral : 26.626 178.611 6332 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.14 % Allowed : 20.17 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2335 helix: 1.52 (0.15), residues: 1302 sheet: -0.66 (0.49), residues: 111 loop : -0.18 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K1151 HIS 0.004 0.001 HIS L 38 PHE 0.030 0.001 PHE K1022 TYR 0.021 0.002 TYR M 373 ARG 0.010 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 1394) hydrogen bonds : angle 3.44346 ( 3678) metal coordination : bond 0.00947 ( 17) metal coordination : angle 2.95490 ( 15) covalent geometry : bond 0.00392 (27486) covalent geometry : angle 0.55576 (38555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18382.69 seconds wall clock time: 316 minutes 36.26 seconds (18996.26 seconds total)