Starting phenix.real_space_refine on Tue Jun 24 09:46:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hy0_35084/06_2025/8hy0_35084_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hy0_35084/06_2025/8hy0_35084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hy0_35084/06_2025/8hy0_35084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hy0_35084/06_2025/8hy0_35084.map" model { file = "/net/cci-nas-00/data/ceres_data/8hy0_35084/06_2025/8hy0_35084_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hy0_35084/06_2025/8hy0_35084_neut.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= 0.002 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 340 5.49 5 S 102 5.16 5 C 17226 2.51 5 N 5098 2.21 5 O 6048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28821 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 837 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3466 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "J" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 3504 Classifications: {'DNA': 170} Link IDs: {'rna3p': 169} Chain: "K" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4597 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 12, 'TRANS': 536} Chain breaks: 2 Chain: "L" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3048 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 365} Chain: "M" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2398 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 281} Chain breaks: 2 Chain: "N" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3073 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 4 Chain: "O" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1275 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "P" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1249 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23908 SG CYS N 263 75.494 93.776 92.040 1.00 58.89 S ATOM 23925 SG CYS N 266 74.616 91.077 89.480 1.00 62.13 S ATOM 24078 SG CYS N 286 77.192 93.761 88.551 1.00 45.24 S ATOM 23989 SG CYS N 275 76.508 103.330 99.753 1.00 85.58 S ATOM 24010 SG CYS N 278 72.529 103.314 99.284 1.00 90.86 S ATOM 24213 SG CYS N 303 74.840 104.681 96.637 1.00 88.55 S ATOM 24236 SG CYS N 306 74.443 106.489 99.878 1.00 98.42 S ATOM 25138 SG CYS N 417 61.690 54.244 67.578 1.00 30.71 S ATOM 25165 SG CYS N 420 61.658 50.519 66.769 1.00 35.54 S ATOM 25421 SG CYS N 451 64.910 52.529 66.471 1.00 46.29 S ATOM 25326 SG CYS N 440 60.466 66.139 69.617 1.00 42.65 S ATOM 25352 SG CYS N 443 57.546 65.738 67.010 1.00 20.36 S ATOM 25541 SG CYS N 466 61.077 64.437 66.076 1.00 59.47 S ATOM 27616 SG CYS P 263 29.608 108.959 29.751 1.00101.72 S ATOM 27633 SG CYS P 266 31.112 109.275 26.277 1.00108.72 S ATOM 27786 SG CYS P 286 29.713 105.852 27.160 1.00 95.81 S ATOM 27697 SG CYS P 275 24.784 106.389 41.257 1.00141.65 S ATOM 27718 SG CYS P 278 28.049 107.182 41.453 1.00142.16 S ATOM 27921 SG CYS P 303 27.780 103.591 40.423 1.00119.98 S ATOM 27944 SG CYS P 306 26.139 104.585 43.706 1.00139.05 S Time building chain proxies: 15.25, per 1000 atoms: 0.53 Number of scatterers: 28821 At special positions: 0 Unit cell: (139.65, 158.55, 199.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 102 16.00 P 340 15.00 O 6048 8.00 N 5098 7.00 C 17226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.42 Conformation dependent library (CDL) restraints added in 3.1 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 " pdb=" ZN P 701 " pdb="ZN ZN P 701 " - pdb=" ND1 HIS P 283 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 266 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 263 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 286 " pdb=" ZN P 702 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 275 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 303 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 278 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 306 " Number of angles added : 24 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 20 sheets defined 58.0% alpha, 5.8% beta 168 base pairs and 299 stacking pairs defined. Time for finding SS restraints: 13.65 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 87 through 114 removed outlier: 3.712A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.545A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.523A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.292A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.660A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 34 through 44 removed outlier: 3.504A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 88 through 99 removed outlier: 3.534A pdb=" N ALA D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.474A pdb=" N GLU D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 113 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.519A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 74 removed outlier: 4.027A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 28 through 37 removed outlier: 3.644A pdb=" N LEU G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.065A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.876A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.916A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 662 through 677 removed outlier: 5.208A pdb=" N PHE K 669 " --> pdb=" O GLU K 665 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU K 670 " --> pdb=" O VAL K 666 " (cutoff:3.500A) Processing helix chain 'K' and resid 678 through 694 Processing helix chain 'K' and resid 698 through 710 Processing helix chain 'K' and resid 715 through 725 removed outlier: 3.625A pdb=" N GLY K 725 " --> pdb=" O LYS K 721 " (cutoff:3.500A) Processing helix chain 'K' and resid 759 through 764 removed outlier: 3.740A pdb=" N PHE K 764 " --> pdb=" O LYS K 760 " (cutoff:3.500A) Processing helix chain 'K' and resid 771 through 778 Processing helix chain 'K' and resid 785 through 790 Processing helix chain 'K' and resid 801 through 840 removed outlier: 4.063A pdb=" N ASN K 840 " --> pdb=" O ASN K 836 " (cutoff:3.500A) Processing helix chain 'K' and resid 852 through 857 removed outlier: 4.311A pdb=" N GLY K 856 " --> pdb=" O PRO K 853 " (cutoff:3.500A) Processing helix chain 'K' and resid 861 through 871 Processing helix chain 'K' and resid 872 through 886 removed outlier: 4.344A pdb=" N PHE K 877 " --> pdb=" O LYS K 873 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU K 878 " --> pdb=" O GLU K 874 " (cutoff:3.500A) Processing helix chain 'K' and resid 886 through 928 removed outlier: 3.645A pdb=" N THR K 890 " --> pdb=" O HIS K 886 " (cutoff:3.500A) Proline residue: K 892 - end of helix removed outlier: 3.759A pdb=" N VAL K 915 " --> pdb=" O GLU K 911 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE K 925 " --> pdb=" O GLN K 921 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYS K 926 " --> pdb=" O LYS K 922 " (cutoff:3.500A) Processing helix chain 'K' and resid 934 through 943 Processing helix chain 'K' and resid 944 through 964 removed outlier: 3.637A pdb=" N ILE K 952 " --> pdb=" O LEU K 948 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE K 964 " --> pdb=" O THR K 960 " (cutoff:3.500A) Processing helix chain 'K' and resid 982 through 999 removed outlier: 3.889A pdb=" N TYR K 986 " --> pdb=" O LYS K 982 " (cutoff:3.500A) Processing helix chain 'K' and resid 1003 through 1022 Processing helix chain 'K' and resid 1025 through 1033 Processing helix chain 'K' and resid 1141 through 1164 removed outlier: 3.534A pdb=" N ILE K1161 " --> pdb=" O ARG K1157 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET K1164 " --> pdb=" O GLU K1160 " (cutoff:3.500A) Processing helix chain 'K' and resid 1164 through 1174 Processing helix chain 'K' and resid 1178 through 1184 Processing helix chain 'K' and resid 1202 through 1216 Processing helix chain 'K' and resid 1220 through 1233 Processing helix chain 'K' and resid 1236 through 1240 Processing helix chain 'K' and resid 1241 through 1258 Processing helix chain 'K' and resid 1262 through 1275 removed outlier: 3.572A pdb=" N MET K1266 " --> pdb=" O THR K1262 " (cutoff:3.500A) Processing helix chain 'K' and resid 1279 through 1292 removed outlier: 3.654A pdb=" N GLN K1283 " --> pdb=" O SER K1279 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 42 through 55 removed outlier: 4.250A pdb=" N ARG L 46 " --> pdb=" O PRO L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.846A pdb=" N LYS L 59 " --> pdb=" O GLY L 56 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET L 61 " --> pdb=" O TYR L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 75 removed outlier: 3.559A pdb=" N MET L 74 " --> pdb=" O THR L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 89 Processing helix chain 'L' and resid 91 through 95 removed outlier: 4.003A pdb=" N LEU L 94 " --> pdb=" O PRO L 91 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU L 95 " --> pdb=" O ASP L 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 91 through 95' Processing helix chain 'L' and resid 98 through 104 Processing helix chain 'L' and resid 115 through 136 Processing helix chain 'L' and resid 164 through 175 Processing helix chain 'L' and resid 190 through 197 Processing helix chain 'L' and resid 226 through 230 removed outlier: 3.521A pdb=" N LYS L 230 " --> pdb=" O GLY L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 263 Proline residue: L 253 - end of helix Processing helix chain 'L' and resid 272 through 276 removed outlier: 3.546A pdb=" N SER L 275 " --> pdb=" O GLY L 272 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 300 removed outlier: 4.115A pdb=" N CYS L 294 " --> pdb=" O GLY L 290 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL L 295 " --> pdb=" O HIS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 329 Processing helix chain 'L' and resid 343 through 347 removed outlier: 3.531A pdb=" N TYR L 347 " --> pdb=" O TYR L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 380 Processing helix chain 'L' and resid 381 through 383 No H-bonds generated for 'chain 'L' and resid 381 through 383' Processing helix chain 'M' and resid 85 through 89 Processing helix chain 'M' and resid 101 through 131 Processing helix chain 'M' and resid 225 through 241 Processing helix chain 'M' and resid 254 through 266 removed outlier: 3.645A pdb=" N GLU M 262 " --> pdb=" O LEU M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 297 removed outlier: 4.770A pdb=" N GLY M 294 " --> pdb=" O ASP M 290 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASN M 295 " --> pdb=" O LYS M 291 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU M 297 " --> pdb=" O LEU M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 316 removed outlier: 4.417A pdb=" N GLN M 305 " --> pdb=" O LEU M 301 " (cutoff:3.500A) Processing helix chain 'M' and resid 327 through 344 removed outlier: 3.689A pdb=" N LEU M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 339 - end of helix Processing helix chain 'M' and resid 348 through 369 removed outlier: 3.988A pdb=" N MET M 368 " --> pdb=" O VAL M 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS M 369 " --> pdb=" O TRP M 365 " (cutoff:3.500A) Processing helix chain 'M' and resid 369 through 374 Processing helix chain 'M' and resid 391 through 401 removed outlier: 4.288A pdb=" N MET M 401 " --> pdb=" O VAL M 397 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 104 Processing helix chain 'N' and resid 120 through 128 removed outlier: 4.696A pdb=" N GLU N 126 " --> pdb=" O LYS N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 175 Processing helix chain 'N' and resid 303 through 315 Processing helix chain 'N' and resid 318 through 330 Processing helix chain 'N' and resid 336 through 343 removed outlier: 3.760A pdb=" N ILE N 343 " --> pdb=" O LEU N 339 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 359 Processing helix chain 'N' and resid 382 through 387 Processing helix chain 'N' and resid 430 through 434 Processing helix chain 'N' and resid 546 through 578 removed outlier: 3.745A pdb=" N PHE N 569 " --> pdb=" O LYS N 565 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU N 571 " --> pdb=" O PHE N 567 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER N 572 " --> pdb=" O GLN N 568 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU N 577 " --> pdb=" O LEU N 573 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL N 578 " --> pdb=" O ILE N 574 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 241 removed outlier: 3.553A pdb=" N LYS O 229 " --> pdb=" O PRO O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 269 removed outlier: 4.282A pdb=" N GLN O 267 " --> pdb=" O HIS O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 271 through 293 Processing helix chain 'O' and resid 302 through 314 Processing helix chain 'O' and resid 327 through 343 removed outlier: 3.717A pdb=" N LEU O 331 " --> pdb=" O GLY O 327 " (cutoff:3.500A) Proline residue: O 339 - end of helix removed outlier: 3.615A pdb=" N SER O 343 " --> pdb=" O PRO O 339 " (cutoff:3.500A) Processing helix chain 'O' and resid 349 through 369 removed outlier: 4.011A pdb=" N HIS O 369 " --> pdb=" O TRP O 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 369 through 374 removed outlier: 4.220A pdb=" N TYR O 373 " --> pdb=" O HIS O 369 " (cutoff:3.500A) Processing helix chain 'P' and resid 303 through 313 Processing helix chain 'P' and resid 315 through 330 removed outlier: 3.713A pdb=" N LEU P 319 " --> pdb=" O SER P 315 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN P 330 " --> pdb=" O PHE P 326 " (cutoff:3.500A) Processing helix chain 'P' and resid 333 through 337 Processing helix chain 'P' and resid 338 through 345 removed outlier: 3.657A pdb=" N ASN P 342 " --> pdb=" O LYS P 338 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE P 343 " --> pdb=" O LEU P 339 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP P 344 " --> pdb=" O LEU P 340 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER P 345 " --> pdb=" O PHE P 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 338 through 345' Processing helix chain 'P' and resid 354 through 359 Processing helix chain 'P' and resid 544 through 580 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.820A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.002A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.598A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.433A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.807A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 756 through 757 Processing sheet with id=AB1, first strand: chain 'K' and resid 975 through 978 removed outlier: 3.703A pdb=" N HIS K1311 " --> pdb=" O ASP K1306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP K1306 " --> pdb=" O HIS K1311 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 233 through 238 removed outlier: 7.680A pdb=" N VAL L 234 " --> pdb=" O VAL L 203 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR L 205 " --> pdb=" O VAL L 234 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL L 236 " --> pdb=" O THR L 205 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER L 207 " --> pdb=" O VAL L 236 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU L 238 " --> pdb=" O SER L 207 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS L 209 " --> pdb=" O LEU L 238 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL L 180 " --> pdb=" O MET L 204 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N CYS L 206 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR L 182 " --> pdb=" O CYS L 206 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE L 208 " --> pdb=" O TYR L 182 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP L 184 " --> pdb=" O PHE L 208 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LYS L 210 " --> pdb=" O ASP L 184 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU L 181 " --> pdb=" O VAL L 268 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLN L 270 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE L 183 " --> pdb=" O GLN L 270 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA L 22 " --> pdb=" O VAL L 143 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL L 21 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR L 64 " --> pdb=" O VAL L 21 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR L 23 " --> pdb=" O TYR L 64 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA L 66 " --> pdb=" O TYR L 23 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE L 63 " --> pdb=" O GLU N 177 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N SER N 179 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG L 65 " --> pdb=" O SER N 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.564A pdb=" N PHE M 78 " --> pdb=" O LEU M 28 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'M' and resid 244 through 246 Processing sheet with id=AB6, first strand: chain 'N' and resid 85 through 87 removed outlier: 3.642A pdb=" N GLU N 86 " --> pdb=" O LYS N 95 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS N 95 " --> pdb=" O GLU N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'N' and resid 365 through 366 Processing sheet with id=AB8, first strand: chain 'N' and resid 437 through 439 Processing sheet with id=AB9, first strand: chain 'N' and resid 473 through 477 Processing sheet with id=AC1, first strand: chain 'N' and resid 505 through 506 removed outlier: 6.961A pdb=" N TYR N 506 " --> pdb=" O GLN P 541 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ASP P 543 " --> pdb=" O TYR N 506 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLN N 521 " --> pdb=" O ILE P 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'P' and resid 273 through 274 removed outlier: 3.825A pdb=" N PHE P 282 " --> pdb=" O LEU P 273 " (cutoff:3.500A) 1109 hydrogen bonds defined for protein. 3225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 429 hydrogen bonds 858 hydrogen bond angles 0 basepair planarities 168 basepair parallelities 299 stacking parallelities Total time for adding SS restraints: 23.05 Time building geometry restraints manager: 8.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4859 1.32 - 1.45: 9268 1.45 - 1.57: 15130 1.57 - 1.69: 680 1.69 - 1.81: 157 Bond restraints: 30094 Sorted by residual: bond pdb=" CA ARG L 44 " pdb=" C ARG L 44 " ideal model delta sigma weight residual 1.522 1.449 0.073 1.37e-02 5.33e+03 2.83e+01 bond pdb=" CA ARG D 96 " pdb=" C ARG D 96 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.29e-02 6.01e+03 2.24e+01 bond pdb=" CA LEU A 82 " pdb=" C LEU A 82 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.26e-02 6.30e+03 2.11e+01 bond pdb=" CA LYS F 79 " pdb=" C LYS F 79 " ideal model delta sigma weight residual 1.521 1.465 0.056 1.27e-02 6.20e+03 1.93e+01 bond pdb=" CA ALA D 107 " pdb=" C ALA D 107 " ideal model delta sigma weight residual 1.523 1.487 0.037 8.40e-03 1.42e+04 1.90e+01 ... (remaining 30089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.01: 41699 4.01 - 8.03: 338 8.03 - 12.04: 25 12.04 - 16.06: 3 16.06 - 20.07: 2 Bond angle restraints: 42067 Sorted by residual: angle pdb=" C ASN N 259 " pdb=" N GLU N 260 " pdb=" CA GLU N 260 " ideal model delta sigma weight residual 122.03 101.96 20.07 2.01e+00 2.48e-01 9.97e+01 angle pdb=" N ILE B 50 " pdb=" CA ILE B 50 " pdb=" C ILE B 50 " ideal model delta sigma weight residual 112.12 104.02 8.10 8.40e-01 1.42e+00 9.30e+01 angle pdb=" N GLU A 133 " pdb=" CA GLU A 133 " pdb=" C GLU A 133 " ideal model delta sigma weight residual 113.97 101.71 12.26 1.28e+00 6.10e-01 9.18e+01 angle pdb=" O ASN N 259 " pdb=" C ASN N 259 " pdb=" N GLU N 260 " ideal model delta sigma weight residual 122.23 134.15 -11.92 1.33e+00 5.65e-01 8.04e+01 angle pdb=" CA ASN N 259 " pdb=" C ASN N 259 " pdb=" N GLU N 260 " ideal model delta sigma weight residual 115.82 102.63 13.19 1.60e+00 3.91e-01 6.80e+01 ... (remaining 42062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 15403 35.95 - 71.89: 1872 71.89 - 107.84: 22 107.84 - 143.79: 1 143.79 - 179.73: 4 Dihedral angle restraints: 17302 sinusoidal: 9403 harmonic: 7899 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual 180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA VAL K 923 " pdb=" C VAL K 923 " pdb=" N PHE K 924 " pdb=" CA PHE K 924 " ideal model delta harmonic sigma weight residual -180.00 -157.78 -22.22 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 17299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3769 0.055 - 0.111: 750 0.111 - 0.166: 114 0.166 - 0.222: 14 0.222 - 0.277: 6 Chirality restraints: 4653 Sorted by residual: chirality pdb=" CB VAL O 337 " pdb=" CA VAL O 337 " pdb=" CG1 VAL O 337 " pdb=" CG2 VAL O 337 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB VAL L 363 " pdb=" CA VAL L 363 " pdb=" CG1 VAL L 363 " pdb=" CG2 VAL L 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB THR D 112 " pdb=" CA THR D 112 " pdb=" OG1 THR D 112 " pdb=" CG2 THR D 112 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 4650 not shown) Planarity restraints: 4165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU N 507 " 0.102 5.00e-02 4.00e+02 1.49e-01 3.55e+01 pdb=" N PRO N 508 " -0.257 5.00e-02 4.00e+02 pdb=" CA PRO N 508 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO N 508 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 101 " -0.026 2.00e-02 2.50e+03 5.19e-02 2.70e+01 pdb=" C VAL A 101 " 0.090 2.00e-02 2.50e+03 pdb=" O VAL A 101 " -0.033 2.00e-02 2.50e+03 pdb=" N ALA A 102 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 72 " -0.024 2.00e-02 2.50e+03 5.11e-02 2.61e+01 pdb=" C ARG A 72 " 0.088 2.00e-02 2.50e+03 pdb=" O ARG A 72 " -0.034 2.00e-02 2.50e+03 pdb=" N GLU A 73 " -0.030 2.00e-02 2.50e+03 ... (remaining 4162 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 775 2.65 - 3.21: 25669 3.21 - 3.78: 52280 3.78 - 4.34: 68889 4.34 - 4.90: 101899 Nonbonded interactions: 249512 Sorted by model distance: nonbonded pdb=" OD1 ASP L 186 " pdb="ZN ZN L 501 " model vdw 2.090 2.230 nonbonded pdb=" OD2 ASP L 274 " pdb="ZN ZN L 501 " model vdw 2.208 2.230 nonbonded pdb=" O ASN K 663 " pdb=" OG1 THR K 667 " model vdw 2.209 3.040 nonbonded pdb=" NH2 ARG B 35 " pdb=" OH TYR B 51 " model vdw 2.220 3.120 nonbonded pdb=" O ARG K1308 " pdb=" OG1 THR K1309 " model vdw 2.260 3.040 ... (remaining 249507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 34 or resid 37 through 134)) selection = (chain 'E' and (resid 12 through 13 or resid 18 or resid 38 through 134)) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = (chain 'H' and resid 29 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.160 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 90.490 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 30119 Z= 0.444 Angle : 0.976 25.415 42091 Z= 0.606 Chirality : 0.047 0.277 4653 Planarity : 0.007 0.149 4165 Dihedral : 23.110 179.735 12190 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 16.83 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.87 (0.15), residues: 2640 helix: -1.16 (0.12), residues: 1420 sheet: -0.37 (0.47), residues: 122 loop : -1.26 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile 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 0.15677 ( 1532) hydrogen bonds : angle 6.60856 ( 4083) metal coordination : bond 0.02699 ( 25) metal coordination : angle 7.46250 ( 24) covalent geometry : bond 0.00667 (30094) covalent geometry : angle 0.95991 (42067) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.7157 (tttt) cc_final: 0.6952 (ttpp) REVERT: B 79 LYS cc_start: 0.7371 (mmmm) cc_final: 0.6911 (mmtp) REVERT: C 41 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7807 (mp0) REVERT: C 73 ASN cc_start: 0.8402 (t0) cc_final: 0.8047 (t0) REVERT: C 92 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7868 (mp0) REVERT: D 46 HIS cc_start: 0.6425 (m-70) cc_final: 0.5835 (m90) REVERT: D 47 PRO cc_start: 0.8473 (Cg_exo) cc_final: 0.7952 (Cg_endo) REVERT: D 81 ASN cc_start: 0.8716 (m110) cc_final: 0.8270 (m110) REVERT: E 52 ARG cc_start: 0.7455 (mtt90) cc_final: 0.7073 (mtm-85) REVERT: E 94 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7534 (mm-30) REVERT: F 27 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7037 (tp-100) REVERT: F 77 LYS cc_start: 0.8470 (mttt) cc_final: 0.8246 (mttm) REVERT: F 79 LYS cc_start: 0.7558 (mttp) cc_final: 0.7236 (mtpp) REVERT: G 36 LYS cc_start: 0.8660 (mttt) cc_final: 0.8272 (mttm) REVERT: G 38 ASN cc_start: 0.8187 (m-40) cc_final: 0.7542 (m-40) REVERT: G 84 GLN cc_start: 0.7695 (tp40) cc_final: 0.7438 (tp40) REVERT: H 65 ASP cc_start: 0.7630 (t0) cc_final: 0.7184 (t0) REVERT: H 82 LYS cc_start: 0.8243 (mttt) cc_final: 0.8039 (mmmt) REVERT: H 84 SER cc_start: 0.7296 (m) cc_final: 0.6459 (p) REVERT: H 90 GLU cc_start: 0.7501 (mp0) cc_final: 0.6543 (mp0) REVERT: K 721 LYS cc_start: 0.7541 (ttpt) cc_final: 0.7220 (tptp) REVERT: K 885 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6579 (mm-30) REVERT: K 904 GLU cc_start: 0.7540 (tt0) cc_final: 0.7091 (tt0) REVERT: K 982 LYS cc_start: 0.7849 (mttt) cc_final: 0.7429 (mmtp) REVERT: K 990 CYS cc_start: 0.7972 (t) cc_final: 0.7436 (t) REVERT: K 1015 LYS cc_start: 0.7101 (mttt) cc_final: 0.6815 (mttm) REVERT: K 1136 PHE cc_start: 0.7997 (m-80) cc_final: 0.7686 (m-80) REVERT: K 1166 GLU cc_start: 0.7627 (pp20) cc_final: 0.7194 (pm20) REVERT: K 1205 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7370 (mttm) REVERT: K 1209 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7384 (ttp-110) REVERT: K 1244 LYS cc_start: 0.7492 (mmtt) cc_final: 0.7187 (mmtm) REVERT: K 1271 LYS cc_start: 0.7976 (mttt) cc_final: 0.7533 (mttp) REVERT: L 28 ASP cc_start: 0.8461 (m-30) cc_final: 0.8239 (m-30) REVERT: L 67 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8101 (ttpp) REVERT: L 95 GLU cc_start: 0.7384 (pm20) cc_final: 0.7107 (pm20) REVERT: L 96 MET cc_start: 0.7474 (ttp) cc_final: 0.6874 (mpp) REVERT: L 98 LYS cc_start: 0.7196 (ptmt) cc_final: 0.6955 (tppt) REVERT: L 220 GLU cc_start: 0.8029 (tp30) cc_final: 0.7769 (tp30) REVERT: L 230 LYS cc_start: 0.8661 (tttm) cc_final: 0.8371 (tttp) REVERT: L 305 MET cc_start: 0.9208 (ptp) cc_final: 0.8863 (ptm) REVERT: L 335 ASP cc_start: 0.7571 (p0) cc_final: 0.6758 (t70) REVERT: M 107 MET cc_start: 0.6546 (ppp) cc_final: 0.6119 (ppp) REVERT: M 111 LEU cc_start: 0.9052 (mt) cc_final: 0.8721 (mt) REVERT: M 275 GLN cc_start: 0.6809 (mm-40) cc_final: 0.6558 (mm110) REVERT: M 353 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6721 (mt0) REVERT: M 357 LYS cc_start: 0.7254 (tmtt) cc_final: 0.6744 (tptt) REVERT: N 121 GLU cc_start: 0.7135 (mp0) cc_final: 0.6564 (mt-10) REVERT: N 267 ASN cc_start: 0.8186 (m110) cc_final: 0.7952 (m-40) REVERT: N 305 GLU cc_start: 0.7072 (tt0) cc_final: 0.6707 (mt-10) REVERT: N 352 GLN cc_start: 0.8180 (mm110) cc_final: 0.7906 (tt0) REVERT: N 375 GLU cc_start: 0.7640 (pt0) cc_final: 0.7300 (pm20) REVERT: N 393 GLN cc_start: 0.7515 (mt0) cc_final: 0.7194 (mt0) REVERT: N 413 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7241 (mmtm) REVERT: N 511 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7943 (mtpt) REVERT: N 560 MET cc_start: 0.7365 (mmm) cc_final: 0.7142 (mmm) REVERT: O 256 MET cc_start: 0.6736 (mmm) cc_final: 0.6530 (mmm) REVERT: O 278 LEU cc_start: 0.8204 (tp) cc_final: 0.7964 (tp) REVERT: P 320 LYS cc_start: 0.8376 (mttt) cc_final: 0.7953 (mtmt) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.4714 time to fit residues: 438.4241 Evaluate side-chains 485 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 151 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 232 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 268 optimal weight: 0.4980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 112 GLN D 46 HIS D 92 GLN E 19 GLN E 68 GLN E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN H 106 HIS K 690 ASN K 694 GLN ** K 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 937 GLN K1150 HIS K1190 GLN L 72 GLN L 362 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 393 GLN N 502 ASN N 517 ASN O 275 GLN O 295 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.195830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.124911 restraints weight = 37142.084| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.02 r_work: 0.3040 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30119 Z= 0.226 Angle : 0.627 11.187 42091 Z= 0.347 Chirality : 0.040 0.194 4653 Planarity : 0.005 0.085 4165 Dihedral : 26.322 177.279 6658 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.12 % Allowed : 18.24 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.41 (0.16), residues: 2640 helix: 0.27 (0.13), residues: 1489 sheet: -0.68 (0.45), residues: 127 loop : -0.90 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K1151 HIS 0.006 0.001 HIS P 283 PHE 0.017 0.002 PHE H 67 TYR 0.034 0.002 TYR H 80 ARG 0.007 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 1532) hydrogen bonds : angle 4.05809 ( 4083) metal coordination : bond 0.01415 ( 25) metal coordination : angle 4.06111 ( 24) covalent geometry : bond 0.00522 (30094) covalent geometry : angle 0.61931 (42067) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 532 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8852 (tp) cc_final: 0.8546 (tp) REVERT: A 81 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7884 (p0) REVERT: A 94 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: B 31 LYS cc_start: 0.8700 (tttt) cc_final: 0.8422 (tttm) REVERT: B 67 ARG cc_start: 0.8259 (ttp80) cc_final: 0.8056 (ttp80) REVERT: B 80 THR cc_start: 0.9217 (m) cc_final: 0.8859 (p) REVERT: C 73 ASN cc_start: 0.8752 (t0) cc_final: 0.8378 (t0) REVERT: C 94 ASN cc_start: 0.8855 (t0) cc_final: 0.8514 (t0) REVERT: C 116 LEU cc_start: 0.8894 (mm) cc_final: 0.8493 (mm) REVERT: D 46 HIS cc_start: 0.8123 (m90) cc_final: 0.7847 (m170) REVERT: D 54 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8838 (mmtt) REVERT: D 65 ASP cc_start: 0.8945 (t0) cc_final: 0.8676 (t0) REVERT: D 90 GLU cc_start: 0.7682 (tt0) cc_final: 0.7419 (tt0) REVERT: D 105 LYS cc_start: 0.8355 (mmmt) cc_final: 0.8146 (mmtm) REVERT: E 79 LYS cc_start: 0.8872 (tttp) cc_final: 0.8576 (tttp) REVERT: E 94 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8314 (mm-30) REVERT: F 27 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8377 (tp40) REVERT: F 74 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7850 (tm-30) REVERT: F 77 LYS cc_start: 0.9190 (mttt) cc_final: 0.8785 (mmmt) REVERT: F 79 LYS cc_start: 0.8698 (mttp) cc_final: 0.8386 (mtpp) REVERT: G 36 LYS cc_start: 0.9322 (mttt) cc_final: 0.8995 (mttm) REVERT: G 38 ASN cc_start: 0.8238 (m-40) cc_final: 0.7635 (m-40) REVERT: G 79 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8812 (mp) REVERT: G 90 ASP cc_start: 0.8083 (t0) cc_final: 0.7636 (t0) REVERT: G 104 GLN cc_start: 0.8561 (mp10) cc_final: 0.8360 (mp10) REVERT: H 32 GLU cc_start: 0.7643 (pt0) cc_final: 0.7327 (pt0) REVERT: H 39 TYR cc_start: 0.7997 (t80) cc_final: 0.7722 (t80) REVERT: H 60 ASN cc_start: 0.8720 (t0) cc_final: 0.8220 (t0) REVERT: H 90 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: K 707 ASP cc_start: 0.8228 (t0) cc_final: 0.7696 (t0) REVERT: K 860 MET cc_start: 0.7975 (mmm) cc_final: 0.7284 (mmt) REVERT: K 871 TYR cc_start: 0.8471 (m-80) cc_final: 0.8240 (m-80) REVERT: K 885 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6880 (tp30) REVERT: K 904 GLU cc_start: 0.8071 (tt0) cc_final: 0.7609 (tt0) REVERT: K 928 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9013 (mp) REVERT: K 982 LYS cc_start: 0.8223 (mttt) cc_final: 0.7755 (mmtp) REVERT: K 986 TYR cc_start: 0.8403 (m-10) cc_final: 0.8177 (m-10) REVERT: K 1008 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6978 (mt-10) REVERT: K 1015 LYS cc_start: 0.7982 (mttt) cc_final: 0.7602 (mttp) REVERT: K 1166 GLU cc_start: 0.8118 (pp20) cc_final: 0.7627 (pm20) REVERT: K 1194 MET cc_start: 0.8414 (mtp) cc_final: 0.8152 (mtt) REVERT: K 1205 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7856 (mttm) REVERT: K 1209 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7791 (ttp-110) REVERT: K 1244 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7715 (mmtm) REVERT: K 1271 LYS cc_start: 0.8065 (mttt) cc_final: 0.7716 (mttm) REVERT: K 1287 ARG cc_start: 0.7442 (ttm-80) cc_final: 0.7137 (ttp80) REVERT: K 1298 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7383 (mt-10) REVERT: K 1310 LEU cc_start: 0.8585 (mp) cc_final: 0.8254 (mt) REVERT: L 60 LYS cc_start: 0.8500 (mttm) cc_final: 0.7798 (mttp) REVERT: L 61 MET cc_start: 0.9031 (ptp) cc_final: 0.8826 (ptp) REVERT: L 95 GLU cc_start: 0.7878 (pm20) cc_final: 0.7675 (pm20) REVERT: L 96 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7935 (mtp) REVERT: L 289 GLU cc_start: 0.8770 (mp0) cc_final: 0.8501 (mp0) REVERT: L 335 ASP cc_start: 0.7948 (p0) cc_final: 0.7201 (t70) REVERT: L 363 VAL cc_start: 0.8968 (p) cc_final: 0.8716 (m) REVERT: M 267 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: M 275 GLN cc_start: 0.7104 (mm-40) cc_final: 0.6833 (mm110) REVERT: M 308 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8097 (mm-30) REVERT: M 353 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7095 (mt0) REVERT: M 357 LYS cc_start: 0.8182 (tmtt) cc_final: 0.7714 (ttpt) REVERT: N 116 ASN cc_start: 0.7973 (m-40) cc_final: 0.7518 (t0) REVERT: N 121 GLU cc_start: 0.7405 (mp0) cc_final: 0.6926 (mt-10) REVERT: N 267 ASN cc_start: 0.8436 (m110) cc_final: 0.8214 (m-40) REVERT: N 292 ASP cc_start: 0.7630 (t70) cc_final: 0.7376 (t70) REVERT: N 305 GLU cc_start: 0.7139 (tt0) cc_final: 0.6623 (mt-10) REVERT: N 352 GLN cc_start: 0.8417 (mm110) cc_final: 0.8066 (tt0) REVERT: N 375 GLU cc_start: 0.8321 (pt0) cc_final: 0.7876 (pm20) REVERT: N 413 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8045 (mmtm) REVERT: N 500 LYS cc_start: 0.8450 (mmtp) cc_final: 0.7997 (mmmt) REVERT: N 512 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8498 (mm) REVERT: N 515 GLN cc_start: 0.8209 (mt0) cc_final: 0.7574 (mm-40) REVERT: N 560 MET cc_start: 0.7392 (mmm) cc_final: 0.7004 (mmm) REVERT: O 256 MET cc_start: 0.6435 (mmm) cc_final: 0.6118 (mmm) REVERT: O 260 LYS cc_start: 0.7371 (ptmt) cc_final: 0.6959 (ptmt) REVERT: O 278 LEU cc_start: 0.7339 (tp) cc_final: 0.7134 (tp) REVERT: O 296 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6862 (mpp) REVERT: O 302 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6641 (mt-10) REVERT: O 308 GLU cc_start: 0.8574 (tp30) cc_final: 0.8285 (tp30) REVERT: O 311 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7680 (mppt) REVERT: P 272 PHE cc_start: 0.6980 (m-80) cc_final: 0.6750 (m-10) REVERT: P 320 LYS cc_start: 0.8231 (mttt) cc_final: 0.7674 (mtmt) REVERT: P 328 LYS cc_start: 0.7659 (tptt) cc_final: 0.7085 (tptt) REVERT: P 351 PHE cc_start: 0.6733 (t80) cc_final: 0.6442 (t80) REVERT: P 557 LYS cc_start: 0.7070 (mmtm) cc_final: 0.6657 (mmtm) outliers start: 75 outliers final: 32 residues processed: 579 average time/residue: 0.4671 time to fit residues: 413.8575 Evaluate side-chains 532 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 490 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1189 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain M residue 267 GLN Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 392 SER Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 78 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 145 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 226 optimal weight: 0.0670 chunk 282 optimal weight: 9.9990 chunk 245 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 37 optimal weight: 40.0000 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN K 678 ASN K 694 GLN K 930 HIS L 76 GLN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 393 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.195290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.124883 restraints weight = 36860.934| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.89 r_work: 0.3017 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 30119 Z= 0.259 Angle : 0.623 11.259 42091 Z= 0.345 Chirality : 0.041 0.184 4653 Planarity : 0.005 0.059 4165 Dihedral : 26.373 178.794 6658 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.08 % Allowed : 17.99 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.09 (0.16), residues: 2640 helix: 0.77 (0.13), residues: 1507 sheet: -0.96 (0.44), residues: 118 loop : -0.79 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K1151 HIS 0.012 0.001 HIS P 283 PHE 0.020 0.002 PHE M 77 TYR 0.024 0.002 TYR H 80 ARG 0.007 0.001 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 1532) hydrogen bonds : angle 3.87697 ( 4083) metal coordination : bond 0.02694 ( 25) metal coordination : angle 4.18282 ( 24) covalent geometry : bond 0.00604 (30094) covalent geometry : angle 0.61504 (42067) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 497 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8797 (tp) cc_final: 0.8560 (tp) REVERT: A 81 ASP cc_start: 0.8053 (p0) cc_final: 0.7766 (p0) REVERT: B 31 LYS cc_start: 0.8587 (tttt) cc_final: 0.8340 (tttm) REVERT: C 73 ASN cc_start: 0.8769 (t0) cc_final: 0.8347 (t0) REVERT: C 116 LEU cc_start: 0.8994 (mm) cc_final: 0.8550 (mm) REVERT: D 39 TYR cc_start: 0.8903 (t80) cc_final: 0.8528 (t80) REVERT: D 54 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8765 (mmtt) REVERT: D 65 ASP cc_start: 0.8962 (t0) cc_final: 0.8706 (t0) REVERT: E 79 LYS cc_start: 0.8891 (tttp) cc_final: 0.8595 (tttp) REVERT: F 77 LYS cc_start: 0.9163 (mttt) cc_final: 0.8830 (mmmt) REVERT: F 79 LYS cc_start: 0.8685 (mttp) cc_final: 0.8416 (mmtm) REVERT: G 36 LYS cc_start: 0.9207 (mttt) cc_final: 0.8955 (mttm) REVERT: G 38 ASN cc_start: 0.8069 (m-40) cc_final: 0.7860 (m-40) REVERT: G 79 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8799 (mp) REVERT: G 84 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8916 (tp-100) REVERT: H 32 GLU cc_start: 0.7560 (pt0) cc_final: 0.7273 (pt0) REVERT: H 39 TYR cc_start: 0.8240 (t80) cc_final: 0.7807 (t80) REVERT: H 60 ASN cc_start: 0.8788 (t0) cc_final: 0.8417 (t0) REVERT: H 82 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8816 (mmtp) REVERT: H 90 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8405 (mt-10) REVERT: H 105 LYS cc_start: 0.8544 (mmtp) cc_final: 0.8290 (mmtm) REVERT: K 670 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: K 707 ASP cc_start: 0.8277 (t0) cc_final: 0.7711 (t0) REVERT: K 850 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7524 (mtpt) REVERT: K 860 MET cc_start: 0.8073 (mmm) cc_final: 0.7496 (mmt) REVERT: K 871 TYR cc_start: 0.8327 (m-80) cc_final: 0.8127 (m-80) REVERT: K 885 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6885 (tp30) REVERT: K 928 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9010 (mp) REVERT: K 982 LYS cc_start: 0.8222 (mttt) cc_final: 0.7681 (mtpt) REVERT: K 986 TYR cc_start: 0.8468 (m-10) cc_final: 0.8163 (m-80) REVERT: K 1008 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6983 (mt-10) REVERT: K 1015 LYS cc_start: 0.7999 (mttt) cc_final: 0.7625 (mttp) REVERT: K 1133 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.5690 (ptt90) REVERT: K 1166 GLU cc_start: 0.7954 (pp20) cc_final: 0.7540 (pm20) REVERT: K 1205 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7911 (mttm) REVERT: K 1244 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7720 (mmtm) REVERT: K 1256 LEU cc_start: 0.8675 (tt) cc_final: 0.8280 (tp) REVERT: K 1271 LYS cc_start: 0.8056 (mttt) cc_final: 0.7647 (ttmm) REVERT: K 1285 ILE cc_start: 0.8752 (tp) cc_final: 0.8510 (tp) REVERT: K 1287 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.7368 (ttp80) REVERT: L 46 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8400 (ptt180) REVERT: L 60 LYS cc_start: 0.8505 (mttm) cc_final: 0.7969 (mttt) REVERT: L 61 MET cc_start: 0.9033 (ptp) cc_final: 0.8773 (ptp) REVERT: L 96 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7764 (mtp) REVERT: L 335 ASP cc_start: 0.7855 (p0) cc_final: 0.7220 (t70) REVERT: L 336 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7499 (mttp) REVERT: M 37 MET cc_start: 0.6584 (mmm) cc_final: 0.6332 (tmm) REVERT: M 111 LEU cc_start: 0.8678 (mt) cc_final: 0.8431 (mp) REVERT: M 238 TYR cc_start: 0.8870 (m-10) cc_final: 0.7783 (m-10) REVERT: M 280 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8261 (tp30) REVERT: M 308 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8099 (mm-30) REVERT: M 353 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7088 (mt0) REVERT: M 357 LYS cc_start: 0.8166 (tmtt) cc_final: 0.7749 (ttpt) REVERT: N 121 GLU cc_start: 0.7419 (mp0) cc_final: 0.6972 (mt-10) REVERT: N 267 ASN cc_start: 0.8451 (m110) cc_final: 0.8231 (m-40) REVERT: N 292 ASP cc_start: 0.7698 (t70) cc_final: 0.7324 (t70) REVERT: N 295 ASN cc_start: 0.8406 (t0) cc_final: 0.7670 (m110) REVERT: N 305 GLU cc_start: 0.7184 (tt0) cc_final: 0.6734 (mt-10) REVERT: N 342 ASN cc_start: 0.7639 (m-40) cc_final: 0.6806 (t0) REVERT: N 375 GLU cc_start: 0.8210 (pt0) cc_final: 0.7885 (pm20) REVERT: N 393 GLN cc_start: 0.8073 (mt0) cc_final: 0.7842 (mp10) REVERT: N 402 ASN cc_start: 0.8535 (m-40) cc_final: 0.8273 (m-40) REVERT: N 436 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8936 (mt) REVERT: N 500 LYS cc_start: 0.8506 (mmtp) cc_final: 0.8066 (mmmt) REVERT: N 512 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8570 (mm) REVERT: N 515 GLN cc_start: 0.8142 (mt0) cc_final: 0.7648 (mm-40) REVERT: N 560 MET cc_start: 0.7272 (mmm) cc_final: 0.6932 (mmm) REVERT: O 260 LYS cc_start: 0.7277 (ptmt) cc_final: 0.6836 (ptmt) REVERT: O 296 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.7127 (ptp) REVERT: O 311 LYS cc_start: 0.8224 (mtmm) cc_final: 0.8005 (mtmm) REVERT: P 272 PHE cc_start: 0.7030 (m-80) cc_final: 0.6828 (m-10) REVERT: P 351 PHE cc_start: 0.7003 (t80) cc_final: 0.6671 (t80) outliers start: 98 outliers final: 62 residues processed: 561 average time/residue: 0.5061 time to fit residues: 431.1386 Evaluate side-chains 544 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 470 time to evaluate : 2.772 ------------------------------------------------------------------------------- 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 61 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1133 ARG Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1189 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 336 LYS Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain M residue 267 GLN 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 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 360 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 436 LEU Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Chi-restraints excluded: chain P residue 555 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 68 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 chunk 265 optimal weight: 40.0000 chunk 109 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 229 optimal weight: 50.0000 chunk 294 optimal weight: 20.0000 chunk 187 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 46 HIS E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 562 GLN O 275 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.199666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129902 restraints weight = 37037.828| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.99 r_work: 0.3162 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 30119 Z= 0.204 Angle : 0.576 8.119 42091 Z= 0.322 Chirality : 0.039 0.184 4653 Planarity : 0.004 0.052 4165 Dihedral : 26.180 178.627 6658 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.37 % Allowed : 18.87 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.49 (0.16), residues: 2640 helix: 1.12 (0.14), residues: 1495 sheet: -0.68 (0.43), residues: 125 loop : -0.65 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 464 HIS 0.005 0.001 HIS P 283 PHE 0.022 0.002 PHE M 17 TYR 0.020 0.002 TYR L 313 ARG 0.007 0.000 ARG M 110 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 1532) hydrogen bonds : angle 3.70948 ( 4083) metal coordination : bond 0.01911 ( 25) metal coordination : angle 2.90509 ( 24) covalent geometry : bond 0.00471 (30094) covalent geometry : angle 0.57160 (42067) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 483 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7936 (p0) cc_final: 0.7675 (p0) REVERT: A 94 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: C 64 GLU cc_start: 0.8030 (tt0) cc_final: 0.7753 (tp30) REVERT: C 73 ASN cc_start: 0.8742 (t0) cc_final: 0.8351 (t0) REVERT: C 94 ASN cc_start: 0.8979 (t0) cc_final: 0.8645 (t0) REVERT: C 116 LEU cc_start: 0.9016 (mm) cc_final: 0.8610 (mm) REVERT: D 39 TYR cc_start: 0.8929 (t80) cc_final: 0.8525 (t80) REVERT: D 90 GLU cc_start: 0.7698 (tt0) cc_final: 0.7468 (tt0) REVERT: D 105 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8339 (mmtm) REVERT: E 50 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7549 (pt0) REVERT: F 77 LYS cc_start: 0.9097 (mttt) cc_final: 0.8845 (mmmt) REVERT: G 36 LYS cc_start: 0.9203 (mttt) cc_final: 0.8958 (mttm) REVERT: G 79 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8767 (mp) REVERT: H 32 GLU cc_start: 0.7550 (pt0) cc_final: 0.7308 (pt0) REVERT: H 39 TYR cc_start: 0.8360 (t80) cc_final: 0.8072 (t80) REVERT: H 60 ASN cc_start: 0.8864 (t0) cc_final: 0.8549 (t0) REVERT: H 82 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8794 (mmtp) REVERT: H 105 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8364 (mmtm) REVERT: K 670 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: K 707 ASP cc_start: 0.8278 (t0) cc_final: 0.7750 (t0) REVERT: K 816 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: K 850 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7607 (mtpt) REVERT: K 860 MET cc_start: 0.8081 (mmm) cc_final: 0.7538 (mmt) REVERT: K 885 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7055 (tp30) REVERT: K 928 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9042 (mp) REVERT: K 982 LYS cc_start: 0.8275 (mttt) cc_final: 0.7785 (mtpt) REVERT: K 986 TYR cc_start: 0.8609 (m-10) cc_final: 0.8317 (m-80) REVERT: K 1008 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7164 (mt-10) REVERT: K 1015 LYS cc_start: 0.8055 (mttt) cc_final: 0.7686 (mttp) REVERT: K 1155 TYR cc_start: 0.9212 (t80) cc_final: 0.8993 (t80) REVERT: K 1166 GLU cc_start: 0.8038 (pp20) cc_final: 0.7617 (pm20) REVERT: K 1179 THR cc_start: 0.8334 (p) cc_final: 0.8117 (m) REVERT: K 1194 MET cc_start: 0.8435 (mtp) cc_final: 0.8077 (mtt) REVERT: K 1259 ASP cc_start: 0.7180 (t70) cc_final: 0.6919 (t0) REVERT: K 1271 LYS cc_start: 0.8111 (mttt) cc_final: 0.7721 (ttmm) REVERT: K 1272 ASP cc_start: 0.8458 (t70) cc_final: 0.8091 (t0) REVERT: K 1285 ILE cc_start: 0.8790 (tp) cc_final: 0.8493 (tp) REVERT: K 1287 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7475 (ttp80) REVERT: L 46 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8255 (ptp-170) REVERT: L 60 LYS cc_start: 0.8576 (mttm) cc_final: 0.7923 (mttp) REVERT: L 61 MET cc_start: 0.8973 (ptp) cc_final: 0.8722 (ptp) REVERT: L 96 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7755 (mtp) REVERT: L 335 ASP cc_start: 0.7888 (p0) cc_final: 0.7236 (t70) REVERT: M 37 MET cc_start: 0.6297 (mmm) cc_final: 0.6063 (tmm) REVERT: M 111 LEU cc_start: 0.8724 (mt) cc_final: 0.8487 (mp) REVERT: M 238 TYR cc_start: 0.8930 (m-10) cc_final: 0.7975 (m-10) REVERT: M 280 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8328 (tp30) REVERT: M 308 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8134 (mm-30) REVERT: M 353 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7235 (mt0) REVERT: M 357 LYS cc_start: 0.8359 (tmtt) cc_final: 0.7964 (tttp) REVERT: N 121 GLU cc_start: 0.7567 (mp0) cc_final: 0.7198 (mt-10) REVERT: N 295 ASN cc_start: 0.8541 (t0) cc_final: 0.8102 (m110) REVERT: N 305 GLU cc_start: 0.7304 (tt0) cc_final: 0.6875 (mt-10) REVERT: N 342 ASN cc_start: 0.7694 (m-40) cc_final: 0.7000 (t0) REVERT: N 375 GLU cc_start: 0.8334 (pt0) cc_final: 0.8076 (pm20) REVERT: N 393 GLN cc_start: 0.8083 (mt0) cc_final: 0.7825 (mp10) REVERT: N 402 ASN cc_start: 0.8596 (m-40) cc_final: 0.8365 (m-40) REVERT: N 512 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8787 (mt) REVERT: N 515 GLN cc_start: 0.8236 (mt0) cc_final: 0.7770 (mm-40) REVERT: N 560 MET cc_start: 0.7185 (mmm) cc_final: 0.6857 (mmm) REVERT: O 260 LYS cc_start: 0.7383 (ptmt) cc_final: 0.6903 (ptmt) REVERT: O 292 CYS cc_start: 0.8110 (OUTLIER) cc_final: 0.6920 (t) REVERT: O 296 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6838 (pmm) REVERT: P 351 PHE cc_start: 0.7139 (t80) cc_final: 0.6831 (t80) outliers start: 81 outliers final: 53 residues processed: 534 average time/residue: 0.4779 time to fit residues: 387.9989 Evaluate side-chains 526 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 461 time to evaluate : 2.595 ------------------------------------------------------------------------------- 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 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 889 VAL Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1199 VAL Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1294 MET Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 360 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 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 360 THR Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 204 optimal weight: 20.0000 chunk 221 optimal weight: 0.8980 chunk 230 optimal weight: 20.0000 chunk 176 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 279 optimal weight: 8.9990 chunk 199 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 27 GLN B 93 GLN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 678 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 GLN M 389 ASN O 275 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.201401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.133442 restraints weight = 36833.511| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.01 r_work: 0.3193 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30119 Z= 0.144 Angle : 0.534 8.586 42091 Z= 0.301 Chirality : 0.037 0.168 4653 Planarity : 0.004 0.048 4165 Dihedral : 25.938 178.454 6658 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.37 % Allowed : 19.95 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.79 (0.16), residues: 2640 helix: 1.38 (0.14), residues: 1490 sheet: -0.65 (0.43), residues: 127 loop : -0.53 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 464 HIS 0.003 0.001 HIS F 75 PHE 0.023 0.001 PHE M 17 TYR 0.023 0.001 TYR E 54 ARG 0.007 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 1532) hydrogen bonds : angle 3.53743 ( 4083) metal coordination : bond 0.01331 ( 25) metal coordination : angle 2.42623 ( 24) covalent geometry : bond 0.00324 (30094) covalent geometry : angle 0.53057 (42067) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 491 time to evaluate : 2.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7847 (p0) cc_final: 0.7622 (p0) REVERT: B 80 THR cc_start: 0.9260 (m) cc_final: 0.8896 (p) REVERT: B 92 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8537 (ttp80) REVERT: C 64 GLU cc_start: 0.8034 (tt0) cc_final: 0.7816 (tp30) REVERT: C 73 ASN cc_start: 0.8774 (t0) cc_final: 0.8380 (t0) REVERT: C 116 LEU cc_start: 0.9030 (mm) cc_final: 0.8609 (mm) REVERT: D 39 TYR cc_start: 0.8771 (t80) cc_final: 0.8304 (t80) REVERT: D 40 LYS cc_start: 0.9006 (mttm) cc_final: 0.8641 (mtmt) REVERT: D 65 ASP cc_start: 0.8727 (t0) cc_final: 0.8496 (t0) REVERT: D 105 LYS cc_start: 0.8475 (mmmt) cc_final: 0.8133 (mmtp) REVERT: E 50 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7359 (pt0) REVERT: F 77 LYS cc_start: 0.9052 (mttt) cc_final: 0.8785 (mmmt) REVERT: G 79 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8718 (mp) REVERT: H 39 TYR cc_start: 0.8324 (t80) cc_final: 0.7941 (t80) REVERT: H 60 ASN cc_start: 0.8799 (t0) cc_final: 0.8467 (t0) REVERT: H 61 SER cc_start: 0.9049 (t) cc_final: 0.8607 (m) REVERT: K 670 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: K 707 ASP cc_start: 0.8203 (t0) cc_final: 0.7706 (t0) REVERT: K 816 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: K 850 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7660 (mtpt) REVERT: K 860 MET cc_start: 0.8025 (mmm) cc_final: 0.7377 (mmt) REVERT: K 885 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6984 (tp30) REVERT: K 896 LYS cc_start: 0.7916 (ttmt) cc_final: 0.7425 (ttpp) REVERT: K 982 LYS cc_start: 0.8217 (mttt) cc_final: 0.7696 (mtpt) REVERT: K 986 TYR cc_start: 0.8460 (m-10) cc_final: 0.8149 (m-10) REVERT: K 1008 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7231 (mt-10) REVERT: K 1015 LYS cc_start: 0.8058 (mttt) cc_final: 0.7703 (mttp) REVERT: K 1166 GLU cc_start: 0.8089 (pp20) cc_final: 0.7669 (pm20) REVERT: K 1167 ARG cc_start: 0.7710 (ttp80) cc_final: 0.7382 (ttm110) REVERT: K 1179 THR cc_start: 0.8270 (p) cc_final: 0.8036 (m) REVERT: K 1194 MET cc_start: 0.8335 (mtp) cc_final: 0.7990 (mtt) REVERT: K 1259 ASP cc_start: 0.7180 (t70) cc_final: 0.6849 (t0) REVERT: K 1271 LYS cc_start: 0.8131 (mttt) cc_final: 0.7734 (ttmm) REVERT: K 1272 ASP cc_start: 0.8403 (t70) cc_final: 0.8037 (t0) REVERT: K 1285 ILE cc_start: 0.8808 (tp) cc_final: 0.8505 (tp) REVERT: K 1287 ARG cc_start: 0.7726 (ttm-80) cc_final: 0.7448 (ttp80) REVERT: L 46 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8246 (ptp-170) REVERT: L 60 LYS cc_start: 0.8434 (mttm) cc_final: 0.7799 (mttp) REVERT: L 61 MET cc_start: 0.8845 (ptp) cc_final: 0.8565 (ptp) REVERT: L 96 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7667 (ttm) REVERT: L 204 MET cc_start: 0.8962 (ttm) cc_final: 0.8714 (tpp) REVERT: L 335 ASP cc_start: 0.7853 (p0) cc_final: 0.7141 (t70) REVERT: M 280 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8231 (tp30) REVERT: M 308 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8094 (mm-30) REVERT: M 353 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7186 (mt0) REVERT: M 357 LYS cc_start: 0.8247 (tmtt) cc_final: 0.7743 (tttp) REVERT: N 121 GLU cc_start: 0.7551 (mp0) cc_final: 0.7192 (mt-10) REVERT: N 295 ASN cc_start: 0.8571 (t0) cc_final: 0.8023 (m110) REVERT: N 305 GLU cc_start: 0.7178 (tt0) cc_final: 0.6738 (mt-10) REVERT: N 342 ASN cc_start: 0.7662 (m-40) cc_final: 0.7014 (t0) REVERT: N 375 GLU cc_start: 0.8258 (pt0) cc_final: 0.7990 (pm20) REVERT: N 393 GLN cc_start: 0.8006 (mt0) cc_final: 0.7796 (mp10) REVERT: N 402 ASN cc_start: 0.8531 (m-40) cc_final: 0.8313 (m-40) REVERT: N 512 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8739 (mt) REVERT: N 515 GLN cc_start: 0.8183 (mt0) cc_final: 0.7641 (mm-40) REVERT: N 560 MET cc_start: 0.7180 (mmm) cc_final: 0.6875 (mmm) REVERT: O 260 LYS cc_start: 0.7381 (ptmt) cc_final: 0.6880 (ptmt) REVERT: O 267 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7286 (mp10) REVERT: O 292 CYS cc_start: 0.8184 (OUTLIER) cc_final: 0.6940 (t) REVERT: O 296 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6952 (pmm) REVERT: P 346 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.6949 (m-70) REVERT: P 351 PHE cc_start: 0.7168 (t80) cc_final: 0.6857 (t80) REVERT: P 554 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7103 (ttpp) outliers start: 81 outliers final: 51 residues processed: 543 average time/residue: 0.5519 time to fit residues: 457.9701 Evaluate side-chains 534 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 469 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1199 VAL Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain M residue 94 TYR Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 346 HIS Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Chi-restraints excluded: chain P residue 560 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 178 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 203 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 225 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 238 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 678 ASN M 18 HIS ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.200371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132246 restraints weight = 37039.968| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.99 r_work: 0.3190 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30119 Z= 0.172 Angle : 0.552 9.682 42091 Z= 0.309 Chirality : 0.038 0.171 4653 Planarity : 0.004 0.046 4165 Dihedral : 25.997 178.411 6658 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.58 % Allowed : 20.20 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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 (0.16), residues: 2640 helix: 1.45 (0.14), residues: 1503 sheet: -0.69 (0.44), residues: 118 loop : -0.50 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 261 HIS 0.004 0.001 HIS E 39 PHE 0.024 0.001 PHE M 17 TYR 0.046 0.002 TYR F 88 ARG 0.006 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 1532) hydrogen bonds : angle 3.55515 ( 4083) metal coordination : bond 0.01308 ( 25) metal coordination : angle 2.48732 ( 24) covalent geometry : bond 0.00397 (30094) covalent geometry : angle 0.54931 (42067) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 484 time to evaluate : 4.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8509 (tpp80) cc_final: 0.8191 (tpt-90) REVERT: C 64 GLU cc_start: 0.8032 (tt0) cc_final: 0.7807 (tp30) REVERT: C 73 ASN cc_start: 0.8715 (t0) cc_final: 0.8328 (t0) REVERT: C 116 LEU cc_start: 0.9024 (mm) cc_final: 0.8598 (mm) REVERT: D 39 TYR cc_start: 0.8817 (t80) cc_final: 0.8393 (t80) REVERT: D 40 LYS cc_start: 0.9012 (mttm) cc_final: 0.8662 (mtmt) REVERT: D 65 ASP cc_start: 0.8794 (t0) cc_final: 0.8542 (t0) REVERT: D 68 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: E 50 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7444 (pt0) REVERT: F 77 LYS cc_start: 0.9049 (mttt) cc_final: 0.8806 (mmmt) REVERT: G 79 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8708 (mp) REVERT: H 32 GLU cc_start: 0.7543 (pt0) cc_final: 0.7338 (pt0) REVERT: H 39 TYR cc_start: 0.8299 (t80) cc_final: 0.7966 (t80) REVERT: H 60 ASN cc_start: 0.8863 (t0) cc_final: 0.8507 (t0) REVERT: H 61 SER cc_start: 0.9036 (t) cc_final: 0.8613 (m) REVERT: K 670 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: K 707 ASP cc_start: 0.8209 (t0) cc_final: 0.7692 (t0) REVERT: K 721 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7526 (mtpp) REVERT: K 816 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: K 860 MET cc_start: 0.8060 (mmm) cc_final: 0.7528 (mmt) REVERT: K 868 ARG cc_start: 0.7926 (mtp-110) cc_final: 0.7466 (mtp85) REVERT: K 885 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7031 (tp30) REVERT: K 896 LYS cc_start: 0.7968 (ttmt) cc_final: 0.7470 (ttpp) REVERT: K 903 GLU cc_start: 0.7870 (pp20) cc_final: 0.7662 (pp20) REVERT: K 982 LYS cc_start: 0.8128 (mttt) cc_final: 0.7711 (mmtp) REVERT: K 986 TYR cc_start: 0.8532 (m-10) cc_final: 0.8203 (m-80) REVERT: K 1008 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7303 (mt-10) REVERT: K 1015 LYS cc_start: 0.8119 (mttt) cc_final: 0.7764 (mttp) REVERT: K 1166 GLU cc_start: 0.8115 (pp20) cc_final: 0.7678 (pm20) REVERT: K 1194 MET cc_start: 0.8364 (mtp) cc_final: 0.8074 (mtt) REVERT: K 1210 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8238 (mt) REVERT: K 1259 ASP cc_start: 0.7282 (t70) cc_final: 0.6926 (t70) REVERT: K 1271 LYS cc_start: 0.8136 (mttt) cc_final: 0.7729 (ttmm) REVERT: K 1272 ASP cc_start: 0.8439 (t70) cc_final: 0.8077 (t0) REVERT: K 1285 ILE cc_start: 0.8783 (tp) cc_final: 0.8471 (tp) REVERT: K 1287 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.7463 (ttp80) REVERT: L 46 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8269 (ptp-170) REVERT: L 60 LYS cc_start: 0.8562 (mttm) cc_final: 0.7905 (mttp) REVERT: L 61 MET cc_start: 0.8896 (ptp) cc_final: 0.8665 (ptp) REVERT: L 96 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7613 (ttm) REVERT: L 335 ASP cc_start: 0.7854 (p0) cc_final: 0.7174 (t70) REVERT: M 111 LEU cc_start: 0.8654 (mt) cc_final: 0.7941 (mt) REVERT: M 238 TYR cc_start: 0.8886 (m-10) cc_final: 0.7838 (m-10) REVERT: M 260 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8099 (ttpp) REVERT: M 280 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8251 (tp30) REVERT: M 308 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8085 (mm-30) REVERT: M 353 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7209 (mt0) REVERT: M 357 LYS cc_start: 0.8344 (tmtt) cc_final: 0.7922 (ttpt) REVERT: N 121 GLU cc_start: 0.7581 (mp0) cc_final: 0.7237 (mt-10) REVERT: N 295 ASN cc_start: 0.8557 (t0) cc_final: 0.8157 (m110) REVERT: N 305 GLU cc_start: 0.7210 (tt0) cc_final: 0.6664 (mt-10) REVERT: N 342 ASN cc_start: 0.7798 (m-40) cc_final: 0.7162 (t0) REVERT: N 375 GLU cc_start: 0.8261 (pt0) cc_final: 0.8025 (pm20) REVERT: N 512 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8789 (mt) REVERT: N 515 GLN cc_start: 0.8189 (mt0) cc_final: 0.7649 (mm-40) REVERT: N 560 MET cc_start: 0.7157 (mmm) cc_final: 0.6842 (mmm) REVERT: O 255 GLU cc_start: 0.6785 (tt0) cc_final: 0.6538 (tt0) REVERT: O 260 LYS cc_start: 0.7457 (ptmt) cc_final: 0.6985 (ptmt) REVERT: O 267 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: O 292 CYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7108 (t) REVERT: O 296 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6970 (pmm) REVERT: O 302 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6696 (mt-10) REVERT: O 308 GLU cc_start: 0.8365 (tp30) cc_final: 0.7949 (tp30) REVERT: O 309 LEU cc_start: 0.8900 (mm) cc_final: 0.8601 (mm) REVERT: O 311 LYS cc_start: 0.8408 (mtmm) cc_final: 0.7924 (tptt) REVERT: P 346 HIS cc_start: 0.7090 (OUTLIER) cc_final: 0.6869 (m-70) REVERT: P 351 PHE cc_start: 0.7281 (t80) cc_final: 0.6941 (t80) outliers start: 86 outliers final: 56 residues processed: 537 average time/residue: 0.6332 time to fit residues: 532.6516 Evaluate side-chains 543 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 471 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 721 LYS Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 889 VAL Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 260 LYS Chi-restraints excluded: chain M residue 266 SER 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 321 VAL Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 278 LEU Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 346 HIS Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 554 LYS Chi-restraints excluded: chain P residue 560 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 237 optimal weight: 0.2980 chunk 256 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 284 optimal weight: 6.9990 chunk 270 optimal weight: 0.0170 overall best weight: 2.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 678 ASN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.198926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.130018 restraints weight = 36748.695| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.95 r_work: 0.3136 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30119 Z= 0.216 Angle : 0.587 10.408 42091 Z= 0.325 Chirality : 0.039 0.199 4653 Planarity : 0.004 0.059 4165 Dihedral : 26.080 178.747 6658 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.87 % Allowed : 20.12 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.84 (0.16), residues: 2640 helix: 1.41 (0.14), residues: 1504 sheet: -0.56 (0.45), residues: 116 loop : -0.54 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 261 HIS 0.004 0.001 HIS K1150 PHE 0.026 0.002 PHE P 311 TYR 0.028 0.002 TYR F 88 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 1532) hydrogen bonds : angle 3.62655 ( 4083) metal coordination : bond 0.01410 ( 25) metal coordination : angle 2.42169 ( 24) covalent geometry : bond 0.00502 (30094) covalent geometry : angle 0.58481 (42067) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 483 time to evaluate : 2.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8588 (tpp80) cc_final: 0.8296 (tpt-90) REVERT: C 73 ASN cc_start: 0.8706 (t0) cc_final: 0.8312 (t0) REVERT: C 92 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7827 (mm-30) REVERT: C 116 LEU cc_start: 0.9059 (mm) cc_final: 0.8614 (mm) REVERT: D 39 TYR cc_start: 0.8889 (t80) cc_final: 0.8497 (t80) REVERT: D 65 ASP cc_start: 0.8880 (t0) cc_final: 0.8613 (t0) REVERT: D 68 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: D 105 LYS cc_start: 0.8611 (mmtm) cc_final: 0.8309 (mmmt) REVERT: E 50 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7526 (pt0) REVERT: F 77 LYS cc_start: 0.9050 (mttt) cc_final: 0.8806 (mmmt) REVERT: G 79 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8741 (mp) REVERT: H 39 TYR cc_start: 0.8319 (t80) cc_final: 0.7920 (t80) REVERT: H 60 ASN cc_start: 0.8902 (t0) cc_final: 0.8455 (t0) REVERT: H 61 SER cc_start: 0.9029 (t) cc_final: 0.8569 (m) REVERT: H 76 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.8361 (ttm-80) REVERT: K 670 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: K 707 ASP cc_start: 0.8299 (t0) cc_final: 0.7796 (t0) REVERT: K 721 LYS cc_start: 0.7936 (mttt) cc_final: 0.7638 (mtpp) REVERT: K 816 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: K 850 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7643 (mtpt) REVERT: K 860 MET cc_start: 0.8129 (mmm) cc_final: 0.7570 (mmt) REVERT: K 885 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7104 (tp30) REVERT: K 896 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7759 (ttpt) REVERT: K 982 LYS cc_start: 0.8231 (mttt) cc_final: 0.7770 (mmtp) REVERT: K 986 TYR cc_start: 0.8660 (m-10) cc_final: 0.8351 (m-80) REVERT: K 1002 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6945 (m-10) REVERT: K 1008 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7334 (mt-10) REVERT: K 1015 LYS cc_start: 0.8135 (mttt) cc_final: 0.7756 (mttp) REVERT: K 1166 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7714 (pm20) REVERT: K 1210 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8262 (mt) REVERT: K 1256 LEU cc_start: 0.8753 (tt) cc_final: 0.8367 (tp) REVERT: K 1259 ASP cc_start: 0.7351 (t70) cc_final: 0.6959 (t70) REVERT: K 1271 LYS cc_start: 0.8133 (mttt) cc_final: 0.7684 (ttmm) REVERT: K 1285 ILE cc_start: 0.8782 (tp) cc_final: 0.8463 (tp) REVERT: K 1287 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7545 (ttp80) REVERT: L 46 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8294 (ptp-170) REVERT: L 60 LYS cc_start: 0.8615 (mttm) cc_final: 0.8124 (mttt) REVERT: L 61 MET cc_start: 0.9011 (ptp) cc_final: 0.8753 (ptp) REVERT: L 335 ASP cc_start: 0.7876 (p0) cc_final: 0.7203 (t70) REVERT: M 111 LEU cc_start: 0.8408 (mt) cc_final: 0.7720 (mt) REVERT: M 238 TYR cc_start: 0.8971 (m-10) cc_final: 0.8004 (m-10) REVERT: M 280 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: M 296 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.7206 (ppp) REVERT: M 308 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8212 (mm-30) REVERT: M 353 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7275 (mt0) REVERT: M 357 LYS cc_start: 0.8374 (tmtt) cc_final: 0.7956 (ttpt) REVERT: N 121 GLU cc_start: 0.7575 (mp0) cc_final: 0.7224 (mt-10) REVERT: N 295 ASN cc_start: 0.8605 (t0) cc_final: 0.8201 (m110) REVERT: N 305 GLU cc_start: 0.7326 (tt0) cc_final: 0.6878 (mt-10) REVERT: N 342 ASN cc_start: 0.7872 (m-40) cc_final: 0.7164 (t0) REVERT: N 375 GLU cc_start: 0.8288 (pt0) cc_final: 0.8013 (pm20) REVERT: N 512 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8808 (mt) REVERT: N 515 GLN cc_start: 0.8241 (mt0) cc_final: 0.7691 (mm-40) REVERT: N 560 MET cc_start: 0.7161 (mmm) cc_final: 0.6851 (mmm) REVERT: O 255 GLU cc_start: 0.6774 (tt0) cc_final: 0.6515 (tt0) REVERT: O 260 LYS cc_start: 0.7450 (ptmt) cc_final: 0.6960 (ptmt) REVERT: O 292 CYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7078 (t) REVERT: O 296 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6855 (pmm) REVERT: O 302 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6736 (mt-10) REVERT: O 308 GLU cc_start: 0.8404 (tp30) cc_final: 0.8024 (tp30) REVERT: O 309 LEU cc_start: 0.8885 (mm) cc_final: 0.8571 (mm) REVERT: O 311 LYS cc_start: 0.8346 (mtmm) cc_final: 0.7888 (tptt) REVERT: P 272 PHE cc_start: 0.7580 (m-10) cc_final: 0.7350 (m-80) REVERT: P 346 HIS cc_start: 0.7063 (OUTLIER) cc_final: 0.6674 (m90) REVERT: P 553 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7243 (t70) outliers start: 93 outliers final: 61 residues processed: 546 average time/residue: 0.4768 time to fit residues: 395.4882 Evaluate side-chains 549 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 472 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 844 ASN Chi-restraints excluded: chain K residue 889 VAL Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1002 TYR Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1166 GLU Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain M residue 18 HIS Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 266 SER 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 321 VAL Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain M residue 401 MET Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain N residue 562 GLN Chi-restraints excluded: chain O residue 226 ILE Chi-restraints excluded: chain O residue 278 LEU Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 268 GLN Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 346 HIS Chi-restraints excluded: chain P residue 553 ASP Chi-restraints excluded: chain P residue 554 LYS Chi-restraints excluded: chain P residue 555 ILE Chi-restraints excluded: chain P residue 560 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 134 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 289 optimal weight: 7.9990 chunk 255 optimal weight: 0.9990 chunk 237 optimal weight: 0.0980 chunk 152 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 273 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 202 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 104 GLN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 678 ASN M 18 HIS ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 562 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 = 0.4274 r_free = 0.4274 target = 0.201771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135892 restraints weight = 37098.042| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.87 r_work: 0.3229 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30119 Z= 0.134 Angle : 0.541 11.291 42091 Z= 0.303 Chirality : 0.037 0.203 4653 Planarity : 0.004 0.042 4165 Dihedral : 25.828 179.256 6658 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.12 % Allowed : 20.87 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 1.06 (0.16), residues: 2640 helix: 1.60 (0.14), residues: 1497 sheet: -0.56 (0.43), residues: 128 loop : -0.43 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 365 HIS 0.004 0.001 HIS M 18 PHE 0.023 0.001 PHE P 311 TYR 0.019 0.001 TYR F 88 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 1532) hydrogen bonds : angle 3.46394 ( 4083) metal coordination : bond 0.01074 ( 25) metal coordination : angle 2.13450 ( 24) covalent geometry : bond 0.00296 (30094) covalent geometry : angle 0.53904 (42067) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 499 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8581 (ttpp) REVERT: B 67 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7820 (ttp80) REVERT: C 73 ASN cc_start: 0.8704 (t0) cc_final: 0.8278 (t0) REVERT: C 92 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7737 (mm-30) REVERT: D 39 TYR cc_start: 0.8697 (t80) cc_final: 0.8236 (t80) REVERT: D 40 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8547 (mtmt) REVERT: D 65 ASP cc_start: 0.8777 (t0) cc_final: 0.8488 (t0) REVERT: D 105 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8154 (mmmt) REVERT: E 50 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7321 (pt0) REVERT: F 77 LYS cc_start: 0.8978 (mttt) cc_final: 0.8683 (mmmt) REVERT: G 71 ARG cc_start: 0.8272 (ttm110) cc_final: 0.7979 (ttp-110) REVERT: G 79 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8695 (mp) REVERT: H 39 TYR cc_start: 0.8098 (t80) cc_final: 0.7636 (t80) REVERT: H 60 ASN cc_start: 0.8664 (t0) cc_final: 0.8273 (t0) REVERT: H 61 SER cc_start: 0.8975 (t) cc_final: 0.8530 (m) REVERT: K 670 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: K 707 ASP cc_start: 0.8103 (t0) cc_final: 0.7566 (t0) REVERT: K 721 LYS cc_start: 0.7787 (mttt) cc_final: 0.7531 (mtpp) REVERT: K 816 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: K 860 MET cc_start: 0.7965 (mmm) cc_final: 0.7304 (mmt) REVERT: K 885 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6878 (tp30) REVERT: K 896 LYS cc_start: 0.7824 (ttmt) cc_final: 0.7325 (ttpp) REVERT: K 928 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8898 (mp) REVERT: K 982 LYS cc_start: 0.8009 (mttt) cc_final: 0.7601 (mmtp) REVERT: K 986 TYR cc_start: 0.8395 (m-80) cc_final: 0.8094 (m-10) REVERT: K 1008 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7110 (mt-10) REVERT: K 1015 LYS cc_start: 0.7951 (mttt) cc_final: 0.7567 (mttp) REVERT: K 1166 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7605 (pm20) REVERT: K 1167 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7425 (ttp80) REVERT: K 1194 MET cc_start: 0.8263 (mtp) cc_final: 0.7875 (mtt) REVERT: K 1210 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8137 (mt) REVERT: K 1259 ASP cc_start: 0.6769 (t70) cc_final: 0.6361 (t70) REVERT: K 1271 LYS cc_start: 0.7983 (mttt) cc_final: 0.7523 (ttmm) REVERT: K 1272 ASP cc_start: 0.7888 (t0) cc_final: 0.7627 (t0) REVERT: K 1285 ILE cc_start: 0.8761 (tp) cc_final: 0.8443 (tp) REVERT: K 1287 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7324 (ttp80) REVERT: L 46 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8192 (ptp-170) REVERT: L 60 LYS cc_start: 0.8533 (mttm) cc_final: 0.7841 (mttp) REVERT: L 61 MET cc_start: 0.8870 (ptp) cc_final: 0.8611 (ptp) REVERT: L 335 ASP cc_start: 0.7835 (p0) cc_final: 0.7074 (t70) REVERT: M 260 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7925 (ttpp) REVERT: M 280 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8147 (tp30) REVERT: M 296 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.7085 (ppp) REVERT: M 308 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8011 (mm-30) REVERT: M 353 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7081 (mt0) REVERT: M 357 LYS cc_start: 0.8143 (tmtt) cc_final: 0.7684 (ttpt) REVERT: N 107 LYS cc_start: 0.7676 (mmtp) cc_final: 0.7239 (mmtp) REVERT: N 121 GLU cc_start: 0.7488 (mp0) cc_final: 0.7128 (mt-10) REVERT: N 295 ASN cc_start: 0.8585 (t0) cc_final: 0.8237 (m110) REVERT: N 305 GLU cc_start: 0.7090 (tt0) cc_final: 0.6656 (mt-10) REVERT: N 342 ASN cc_start: 0.7653 (m-40) cc_final: 0.7044 (t0) REVERT: N 506 TYR cc_start: 0.8065 (t80) cc_final: 0.7816 (t80) REVERT: N 512 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8762 (mt) REVERT: N 515 GLN cc_start: 0.8092 (mt0) cc_final: 0.7492 (mm-40) REVERT: N 560 MET cc_start: 0.7131 (mmm) cc_final: 0.6824 (mmm) REVERT: O 255 GLU cc_start: 0.6753 (tt0) cc_final: 0.6500 (tt0) REVERT: O 260 LYS cc_start: 0.7362 (ptmt) cc_final: 0.6858 (ptmt) REVERT: O 267 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7149 (mp10) REVERT: O 292 CYS cc_start: 0.7999 (OUTLIER) cc_final: 0.6854 (t) REVERT: O 296 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6641 (pmm) REVERT: O 302 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6705 (mt-10) REVERT: O 308 GLU cc_start: 0.8429 (tp30) cc_final: 0.8034 (tp30) REVERT: O 309 LEU cc_start: 0.8877 (mm) cc_final: 0.8555 (mm) REVERT: O 311 LYS cc_start: 0.8376 (mtmm) cc_final: 0.7871 (tptt) REVERT: P 351 PHE cc_start: 0.6830 (t80) cc_final: 0.6606 (t80) REVERT: P 553 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6941 (t70) REVERT: P 554 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7036 (ttpp) outliers start: 75 outliers final: 48 residues processed: 543 average time/residue: 0.5976 time to fit residues: 493.3220 Evaluate side-chains 550 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 485 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 844 ASN Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1019 SER Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1166 GLU Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1239 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain M residue 260 LYS Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain N residue 562 GLN Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 278 LEU Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 268 GLN Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 553 ASP Chi-restraints excluded: chain P residue 554 LYS Chi-restraints excluded: chain P residue 557 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 122 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 272 optimal weight: 8.9990 chunk 281 optimal weight: 30.0000 chunk 291 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 182 optimal weight: 0.0980 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.198837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.129818 restraints weight = 36663.910| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.07 r_work: 0.3091 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 30119 Z= 0.229 Angle : 0.600 10.219 42091 Z= 0.331 Chirality : 0.040 0.286 4653 Planarity : 0.004 0.045 4165 Dihedral : 26.048 179.383 6658 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.96 % Allowed : 21.57 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.96 (0.16), residues: 2640 helix: 1.50 (0.14), residues: 1504 sheet: -0.51 (0.46), residues: 116 loop : -0.47 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 261 HIS 0.004 0.001 HIS L 209 PHE 0.024 0.002 PHE M 17 TYR 0.022 0.002 TYR F 88 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 1532) hydrogen bonds : angle 3.63333 ( 4083) metal coordination : bond 0.01395 ( 25) metal coordination : angle 2.37900 ( 24) covalent geometry : bond 0.00534 (30094) covalent geometry : angle 0.59784 (42067) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 488 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7877 (ttp80) REVERT: C 56 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8100 (tm-30) REVERT: C 73 ASN cc_start: 0.8743 (t0) cc_final: 0.8315 (t0) REVERT: C 92 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7836 (mm-30) REVERT: D 40 LYS cc_start: 0.9008 (mtpp) cc_final: 0.8576 (mtmt) REVERT: D 65 ASP cc_start: 0.8986 (t0) cc_final: 0.8672 (t0) REVERT: D 105 LYS cc_start: 0.8624 (mmtm) cc_final: 0.8292 (mmmt) REVERT: E 50 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: F 64 ASN cc_start: 0.8737 (m-40) cc_final: 0.8487 (m110) REVERT: G 79 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8810 (mp) REVERT: H 39 TYR cc_start: 0.8278 (t80) cc_final: 0.7863 (t80) REVERT: H 60 ASN cc_start: 0.8874 (t0) cc_final: 0.8454 (t0) REVERT: H 61 SER cc_start: 0.9024 (t) cc_final: 0.8592 (m) REVERT: K 670 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: K 707 ASP cc_start: 0.8300 (t0) cc_final: 0.7769 (t0) REVERT: K 721 LYS cc_start: 0.7889 (mttt) cc_final: 0.7598 (mtpp) REVERT: K 756 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8118 (pttt) REVERT: K 816 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: K 850 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7602 (mtpt) REVERT: K 860 MET cc_start: 0.8155 (mmm) cc_final: 0.7567 (mmt) REVERT: K 885 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7132 (tp30) REVERT: K 896 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7528 (ttpp) REVERT: K 928 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9075 (mp) REVERT: K 982 LYS cc_start: 0.8175 (mttt) cc_final: 0.7713 (mmtp) REVERT: K 986 TYR cc_start: 0.8573 (m-80) cc_final: 0.8239 (m-80) REVERT: K 1008 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7351 (mt-10) REVERT: K 1015 LYS cc_start: 0.8120 (mttt) cc_final: 0.7655 (mttp) REVERT: K 1166 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: K 1167 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7649 (ttp80) REVERT: K 1210 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8283 (mt) REVERT: K 1259 ASP cc_start: 0.7367 (t70) cc_final: 0.6951 (t70) REVERT: K 1271 LYS cc_start: 0.8127 (mttt) cc_final: 0.7670 (ttmm) REVERT: K 1272 ASP cc_start: 0.8140 (t0) cc_final: 0.7774 (t0) REVERT: K 1285 ILE cc_start: 0.8754 (tp) cc_final: 0.8433 (tp) REVERT: K 1287 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7547 (ttp80) REVERT: L 46 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8462 (ptt180) REVERT: L 60 LYS cc_start: 0.8670 (mttm) cc_final: 0.8175 (mttt) REVERT: L 61 MET cc_start: 0.9084 (ptp) cc_final: 0.8835 (ptp) REVERT: L 98 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7907 (tttt) REVERT: L 335 ASP cc_start: 0.7919 (p0) cc_final: 0.7213 (t70) REVERT: M 238 TYR cc_start: 0.8997 (m-10) cc_final: 0.8017 (m-10) REVERT: M 260 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8127 (ttpp) REVERT: M 280 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8372 (tp30) REVERT: M 296 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.7322 (ppp) REVERT: M 308 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8275 (mm-30) REVERT: M 353 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7294 (mt0) REVERT: M 357 LYS cc_start: 0.8466 (tmtt) cc_final: 0.8062 (ttpt) REVERT: N 107 LYS cc_start: 0.7783 (mmtp) cc_final: 0.6630 (ttmt) REVERT: N 121 GLU cc_start: 0.7567 (mp0) cc_final: 0.7191 (mt-10) REVERT: N 295 ASN cc_start: 0.8636 (t0) cc_final: 0.8284 (m110) REVERT: N 305 GLU cc_start: 0.7329 (tt0) cc_final: 0.6823 (mt-10) REVERT: N 342 ASN cc_start: 0.7923 (m-40) cc_final: 0.7199 (t0) REVERT: N 512 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8857 (mt) REVERT: N 515 GLN cc_start: 0.8229 (mt0) cc_final: 0.7650 (mm-40) REVERT: N 560 MET cc_start: 0.7124 (mmm) cc_final: 0.6798 (mmm) REVERT: O 255 GLU cc_start: 0.6757 (tt0) cc_final: 0.6509 (tt0) REVERT: O 260 LYS cc_start: 0.7418 (ptmt) cc_final: 0.6913 (ptmt) REVERT: O 292 CYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7087 (t) REVERT: O 296 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6778 (pmm) REVERT: O 302 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6734 (mt-10) REVERT: O 308 GLU cc_start: 0.8466 (tp30) cc_final: 0.8111 (tp30) REVERT: O 309 LEU cc_start: 0.8876 (mm) cc_final: 0.8548 (mm) REVERT: P 346 HIS cc_start: 0.7007 (OUTLIER) cc_final: 0.6564 (m90) REVERT: P 351 PHE cc_start: 0.7129 (t80) cc_final: 0.6906 (t80) REVERT: P 553 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7250 (t70) outliers start: 71 outliers final: 48 residues processed: 532 average time/residue: 0.5079 time to fit residues: 407.7505 Evaluate side-chains 548 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 482 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 756 LYS Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 844 ASN Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1166 GLU Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain M residue 18 HIS Chi-restraints excluded: chain M residue 260 LYS Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 292 CYS Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 343 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain N residue 512 ILE Chi-restraints excluded: chain N residue 562 GLN Chi-restraints excluded: chain O residue 278 LEU Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 346 HIS Chi-restraints excluded: chain P residue 553 ASP Chi-restraints excluded: chain P residue 554 LYS Chi-restraints excluded: chain P residue 557 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 162 optimal weight: 0.2980 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 237 optimal weight: 0.8980 chunk 205 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** C 104 GLN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 678 ASN L 341 ASN M 18 HIS ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.201855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.132458 restraints weight = 36877.821| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.00 r_work: 0.3118 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30119 Z= 0.135 Angle : 0.552 11.764 42091 Z= 0.307 Chirality : 0.037 0.164 4653 Planarity : 0.004 0.041 4165 Dihedral : 25.799 179.807 6658 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.50 % Allowed : 22.03 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.16), residues: 2640 helix: 1.67 (0.14), residues: 1497 sheet: -0.58 (0.43), residues: 128 loop : -0.41 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 365 HIS 0.003 0.001 HIS D 46 PHE 0.022 0.001 PHE P 311 TYR 0.015 0.001 TYR L 313 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 1532) hydrogen bonds : angle 3.48680 ( 4083) metal coordination : bond 0.00946 ( 25) metal coordination : angle 2.06685 ( 24) covalent geometry : bond 0.00300 (30094) covalent geometry : angle 0.55014 (42067) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 485 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8407 (tpp80) cc_final: 0.7956 (tpt90) REVERT: C 73 ASN cc_start: 0.8753 (t0) cc_final: 0.8332 (t0) REVERT: C 92 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7797 (mm-30) REVERT: D 39 TYR cc_start: 0.8789 (t80) cc_final: 0.8440 (t80) REVERT: D 40 LYS cc_start: 0.9033 (mtpp) cc_final: 0.8493 (mtmt) REVERT: D 65 ASP cc_start: 0.8848 (t0) cc_final: 0.8625 (t0) REVERT: D 105 LYS cc_start: 0.8604 (mmtm) cc_final: 0.8254 (mmmt) REVERT: E 50 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7426 (pt0) REVERT: E 90 MET cc_start: 0.8585 (tpp) cc_final: 0.8318 (mmp) REVERT: F 88 TYR cc_start: 0.7310 (m-80) cc_final: 0.7107 (m-80) REVERT: G 79 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8757 (mp) REVERT: H 39 TYR cc_start: 0.8170 (t80) cc_final: 0.7694 (t80) REVERT: H 60 ASN cc_start: 0.8706 (t0) cc_final: 0.8339 (t0) REVERT: H 61 SER cc_start: 0.9000 (t) cc_final: 0.8604 (m) REVERT: K 670 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: K 707 ASP cc_start: 0.8254 (t0) cc_final: 0.7736 (t0) REVERT: K 710 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8051 (mt) REVERT: K 721 LYS cc_start: 0.7833 (mttt) cc_final: 0.7599 (mtpp) REVERT: K 756 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.7920 (pttt) REVERT: K 816 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: K 850 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7624 (mtpt) REVERT: K 885 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7026 (tp30) REVERT: K 896 LYS cc_start: 0.7963 (ttmt) cc_final: 0.7486 (ttpp) REVERT: K 928 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8914 (mp) REVERT: K 982 LYS cc_start: 0.8092 (mttt) cc_final: 0.7685 (mmtp) REVERT: K 986 TYR cc_start: 0.8517 (m-80) cc_final: 0.8198 (m-10) REVERT: K 1008 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7069 (pt0) REVERT: K 1015 LYS cc_start: 0.8010 (mttt) cc_final: 0.7593 (mttp) REVERT: K 1166 GLU cc_start: 0.8194 (pp20) cc_final: 0.7725 (pm20) REVERT: K 1167 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7540 (ttp80) REVERT: K 1194 MET cc_start: 0.8312 (mtp) cc_final: 0.7920 (mtt) REVERT: K 1210 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8245 (mt) REVERT: K 1259 ASP cc_start: 0.6792 (t70) cc_final: 0.6378 (t70) REVERT: K 1271 LYS cc_start: 0.7958 (mttt) cc_final: 0.7472 (ttpp) REVERT: K 1272 ASP cc_start: 0.7983 (t0) cc_final: 0.7708 (t0) REVERT: K 1285 ILE cc_start: 0.8730 (tp) cc_final: 0.8403 (tp) REVERT: K 1287 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7446 (ttp80) REVERT: L 46 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8265 (ptp-170) REVERT: L 60 LYS cc_start: 0.8615 (mttm) cc_final: 0.7943 (mttp) REVERT: L 61 MET cc_start: 0.8916 (ptp) cc_final: 0.8652 (ptp) REVERT: L 88 ARG cc_start: 0.8655 (mtm-85) cc_final: 0.8444 (mtp-110) REVERT: L 289 GLU cc_start: 0.8682 (mp0) cc_final: 0.8273 (mp0) REVERT: L 335 ASP cc_start: 0.7913 (p0) cc_final: 0.7139 (t70) REVERT: M 260 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8058 (ttpp) REVERT: M 280 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8275 (tp30) REVERT: M 296 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.7208 (ppp) REVERT: M 308 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8368 (mm-30) REVERT: M 353 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7192 (mt0) REVERT: M 357 LYS cc_start: 0.8287 (tmtt) cc_final: 0.7884 (ttpt) REVERT: N 107 LYS cc_start: 0.7647 (mmtp) cc_final: 0.7196 (mmtp) REVERT: N 121 GLU cc_start: 0.7539 (mp0) cc_final: 0.7142 (mt-10) REVERT: N 295 ASN cc_start: 0.8615 (t0) cc_final: 0.8258 (m110) REVERT: N 305 GLU cc_start: 0.7215 (tt0) cc_final: 0.6760 (mt-10) REVERT: N 342 ASN cc_start: 0.7746 (m-40) cc_final: 0.7009 (t0) REVERT: N 515 GLN cc_start: 0.8188 (mt0) cc_final: 0.7604 (mm-40) REVERT: O 244 LYS cc_start: 0.4032 (tptp) cc_final: 0.3767 (tptp) REVERT: O 260 LYS cc_start: 0.7417 (ptmt) cc_final: 0.6886 (ptmt) REVERT: O 292 CYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7011 (t) REVERT: O 296 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6875 (pmm) REVERT: O 309 LEU cc_start: 0.8876 (mm) cc_final: 0.8637 (mm) REVERT: P 346 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6652 (m90) REVERT: P 349 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7154 (mtmt) REVERT: P 351 PHE cc_start: 0.7019 (t80) cc_final: 0.6762 (t80) REVERT: P 553 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.6506 (t70) REVERT: P 554 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7135 (ttpp) REVERT: P 557 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6782 (mttp) outliers start: 60 outliers final: 39 residues processed: 521 average time/residue: 0.5299 time to fit residues: 411.6515 Evaluate side-chains 535 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 477 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 670 GLU Chi-restraints excluded: chain K residue 671 LYS Chi-restraints excluded: chain K residue 699 LEU Chi-restraints excluded: chain K residue 710 LEU Chi-restraints excluded: chain K residue 712 SER Chi-restraints excluded: chain K residue 756 LYS Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 844 ASN Chi-restraints excluded: chain K residue 893 VAL Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 928 LEU Chi-restraints excluded: chain K residue 952 ILE Chi-restraints excluded: chain K residue 1142 THR Chi-restraints excluded: chain K residue 1178 VAL Chi-restraints excluded: chain K residue 1188 SER Chi-restraints excluded: chain K residue 1210 LEU Chi-restraints excluded: chain K residue 1304 GLU Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 360 MET Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 260 LYS Chi-restraints excluded: chain M residue 280 GLU Chi-restraints excluded: chain M residue 295 ASN Chi-restraints excluded: chain M residue 296 MET Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 172 THR Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 562 GLN Chi-restraints excluded: chain O residue 278 LEU Chi-restraints excluded: chain O residue 292 CYS Chi-restraints excluded: chain O residue 296 MET Chi-restraints excluded: chain P residue 319 LEU Chi-restraints excluded: chain P residue 346 HIS Chi-restraints excluded: chain P residue 349 LYS Chi-restraints excluded: chain P residue 553 ASP Chi-restraints excluded: chain P residue 554 LYS Chi-restraints excluded: chain P residue 557 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 54 optimal weight: 0.6980 chunk 280 optimal weight: 10.0000 chunk 120 optimal weight: 0.5980 chunk 90 optimal weight: 30.0000 chunk 185 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 162 optimal weight: 0.0170 chunk 115 optimal weight: 0.5980 chunk 212 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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** C 31 HIS E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 678 ASN M 18 HIS ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.202732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.134410 restraints weight = 36946.170| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.97 r_work: 0.3229 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30119 Z= 0.131 Angle : 0.544 11.457 42091 Z= 0.302 Chirality : 0.036 0.160 4653 Planarity : 0.004 0.041 4165 Dihedral : 25.733 179.995 6658 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.54 % Allowed : 22.03 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.17), residues: 2640 helix: 1.77 (0.14), residues: 1497 sheet: -0.56 (0.43), residues: 128 loop : -0.37 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 365 HIS 0.003 0.001 HIS L 78 PHE 0.022 0.001 PHE P 311 TYR 0.015 0.001 TYR L 313 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 1532) hydrogen bonds : angle 3.40818 ( 4083) metal coordination : bond 0.00944 ( 25) metal coordination : angle 2.02699 ( 24) covalent geometry : bond 0.00290 (30094) covalent geometry : angle 0.54171 (42067) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23580.81 seconds wall clock time: 416 minutes 13.88 seconds (24973.88 seconds total)