Starting phenix.real_space_refine on Sat Sep 12 19:47:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t9l_10415/09_2026/6t9l_10415.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t9l_10415/09_2026/6t9l_10415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6t9l_10415/09_2026/6t9l_10415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t9l_10415/09_2026/6t9l_10415.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t9l_10415/09_2026/6t9l_10415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t9l_10415/09_2026/6t9l_10415.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6t9l_10415/09_2026/6t9l_10415.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t9l_10415/09_2026/6t9l_10415.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 8 6.06 5 P 288 5.49 5 S 58 5.16 5 C 10515 2.51 5 N 3304 2.21 5 O 3984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18157 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3560 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 431} Chain breaks: 3 Chain: "L" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "M" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 718 Classifications: {'peptide': 90} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 86} Chain: "N" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 663 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 7, 'TRANS': 74} Chain breaks: 1 Chain: "O" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' ZN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12247 SG CYS K 46 20.335 121.114 83.464 1.00559.10 S ATOM 12264 SG CYS K 49 21.461 124.114 81.327 1.00552.89 S ATOM 12400 SG CYS K 68 24.337 123.088 84.113 1.00570.25 S ATOM 12346 SG CYS K 60 18.493 111.899 91.515 1.00554.36 S ATOM 12369 SG CYS K 63 15.108 112.316 90.947 1.00539.82 S ATOM 12627 SG CYS K 96 29.738 112.405 98.879 1.00559.36 S ATOM 12653 SG CYS K 99 32.641 112.804 101.346 1.00562.68 S ATOM 13245 SG CYS K 174 44.447 71.445 76.629 1.00460.20 S ATOM 13308 SG CYS K 182 48.138 73.639 73.714 1.00406.32 S ATOM 13331 SG CYS K 185 47.354 73.231 77.816 1.00408.46 S ATOM 13914 SG CYS K 271 40.324 79.219 64.060 1.00469.68 S ATOM 13929 SG CYS K 273 42.915 81.466 65.469 1.00458.01 S ATOM 14065 SG CYS K 292 38.642 99.115 26.685 1.00613.19 S ATOM 14456 SG CYS K 339 42.734 96.444 25.849 1.00634.00 S ATOM 16715 SG CYS M 73 66.148 69.407 83.582 1.00343.41 S ATOM 16738 SG CYS M 76 68.791 66.531 84.276 1.00347.20 S ATOM 17397 SG CYS N 78 41.792 80.510 94.198 1.00404.65 S ATOM 17421 SG CYS N 81 43.482 78.935 91.255 1.00394.45 S ATOM 17548 SG CYS N 98 40.348 76.993 93.985 1.00457.16 S Time building chain proxies: 3.67, per 1000 atoms: 0.20 Number of scatterers: 18157 At special positions: 0 Unit cell: (146.59, 146.59, 123.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 58 16.00 P 288 15.00 O 3984 8.00 N 3304 7.00 C 10515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 576.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 501 " pdb="ZN ZN K 501 " - pdb=" SG CYS K 46 " pdb="ZN ZN K 501 " - pdb=" SG CYS K 68 " pdb="ZN ZN K 501 " - pdb=" SG CYS K 49 " pdb="ZN ZN K 501 " - pdb=" ND1 HIS K 73 " pdb=" ZN K 502 " pdb="ZN ZN K 502 " - pdb=" NE2 HIS K 83 " pdb="ZN ZN K 502 " - pdb=" SG CYS K 60 " pdb="ZN ZN K 502 " - pdb=" SG CYS K 63 " pdb="ZN ZN K 502 " - pdb=" NE2 HIS K 77 " pdb=" ZN K 503 " pdb="ZN ZN K 503 " - pdb=" ND1 HIS K 6 " pdb="ZN ZN K 503 " - pdb=" SG CYS K 99 " pdb="ZN ZN K 503 " - pdb=" SG CYS K 96 " pdb=" ZN K 504 " pdb="ZN ZN K 504 " - pdb=" NE2 HIS K 170 " pdb="ZN ZN K 504 " - pdb=" SG CYS K 185 " pdb="ZN ZN K 504 " - pdb=" SG CYS K 182 " pdb="ZN ZN K 504 " - pdb=" SG CYS K 174 " pdb=" ZN K 505 " pdb="ZN ZN K 505 " - pdb=" ND1 HIS K 250 " pdb="ZN ZN K 505 " - pdb=" ND1 HIS K 276 " pdb="ZN ZN K 505 " - pdb=" SG CYS K 273 " pdb="ZN ZN K 505 " - pdb=" SG CYS K 271 " pdb=" ZN K 506 " pdb="ZN ZN K 506 " - pdb=" SG CYS K 339 " pdb="ZN ZN K 506 " - pdb=" SG CYS K 292 " pdb=" ZN M 101 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 76 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 73 " pdb=" ZN N 701 " pdb="ZN ZN N 701 " - pdb=" NE2 HIS N 93 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 81 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 98 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 78 " Number of angles added : 13 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2892 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 16 sheets defined 58.4% alpha, 7.8% beta 145 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.006A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.565A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.631A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.440A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.038A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.549A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.708A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.488A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.615A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.547A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.906A 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 79 removed outlier: 3.973A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.911A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.730A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.565A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 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 removed outlier: 3.639A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 4 through 11 removed outlier: 3.675A pdb=" N VAL K 10 " --> pdb=" O HIS K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 32 removed outlier: 3.791A pdb=" N ASN K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 43 removed outlier: 3.846A pdb=" N PHE K 40 " --> pdb=" O PRO K 36 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU K 41 " --> pdb=" O LYS K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.596A pdb=" N SER K 78 " --> pdb=" O PHE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 111 removed outlier: 3.524A pdb=" N ASN K 110 " --> pdb=" O ILE K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 115 Processing helix chain 'K' and resid 117 through 124 removed outlier: 3.526A pdb=" N VAL K 121 " --> pdb=" O TYR K 117 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS K 122 " --> pdb=" O TRP K 118 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR K 123 " --> pdb=" O ASP K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 157 removed outlier: 3.778A pdb=" N SER K 150 " --> pdb=" O CYS K 146 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE K 151 " --> pdb=" O PHE K 147 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS K 154 " --> pdb=" O SER K 150 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU K 155 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS K 157 " --> pdb=" O GLN K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 167 Processing helix chain 'K' and resid 182 through 196 removed outlier: 3.549A pdb=" N LYS K 189 " --> pdb=" O CYS K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 227 removed outlier: 3.681A pdb=" N ILE K 217 " --> pdb=" O GLN K 213 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR K 218 " --> pdb=" O THR K 214 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU K 219 " --> pdb=" O GLY K 215 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU K 220 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS K 225 " --> pdb=" O THR K 221 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE K 226 " --> pdb=" O CYS K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 231 Processing helix chain 'K' and resid 238 through 256 removed outlier: 3.541A pdb=" N ASN K 247 " --> pdb=" O GLN K 243 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS K 250 " --> pdb=" O ILE K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 325 Processing helix chain 'K' and resid 388 through 392 removed outlier: 3.779A pdb=" N TYR K 391 " --> pdb=" O MET K 388 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS K 392 " --> pdb=" O LYS K 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 388 through 392' Processing helix chain 'K' and resid 451 through 456 removed outlier: 3.865A pdb=" N VAL K 455 " --> pdb=" O SER K 451 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU K 456 " --> pdb=" O GLN K 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 451 through 456' Processing helix chain 'L' and resid 7 through 19 removed outlier: 3.574A pdb=" N VAL L 17 " --> pdb=" O GLN L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 36 removed outlier: 4.209A pdb=" N LEU L 24 " --> pdb=" O GLY L 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER L 26 " --> pdb=" O TYR L 22 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 54 removed outlier: 3.620A pdb=" N ASN L 51 " --> pdb=" O LYS L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 69 removed outlier: 3.882A pdb=" N THR L 64 " --> pdb=" O GLN L 60 " (cutoff:3.500A) Proline residue: L 67 - end of helix Processing helix chain 'L' and resid 74 through 90 removed outlier: 3.770A pdb=" N THR L 80 " --> pdb=" O SER L 76 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL L 81 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU L 87 " --> pdb=" O LYS L 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 42 removed outlier: 4.158A pdb=" N ILE M 11 " --> pdb=" O THR M 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY M 14 " --> pdb=" O SER M 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG M 30 " --> pdb=" O ASP M 26 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 93 removed outlier: 3.714A pdb=" N GLN M 90 " --> pdb=" O ALA M 86 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG M 91 " --> pdb=" O ALA M 87 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU M 93 " --> pdb=" O LEU M 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 18 removed outlier: 3.997A pdb=" N GLU N 18 " --> pdb=" O LYS N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 34 Processing helix chain 'N' and resid 35 through 40 Processing helix chain 'N' and resid 51 through 58 removed outlier: 3.859A pdb=" N LYS N 55 " --> pdb=" O ARG N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 88 No H-bonds generated for 'chain 'N' and resid 86 through 88' Processing helix chain 'N' and resid 89 through 97 removed outlier: 3.645A pdb=" N HIS N 93 " --> pdb=" O ALA N 89 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU N 95 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN N 96 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 35 removed outlier: 3.900A pdb=" N VAL O 26 " --> pdb=" O THR O 22 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN O 31 " --> pdb=" O LYS O 27 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS O 33 " --> pdb=" O LYS O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 60 removed outlier: 3.555A pdb=" N ASN O 60 " --> pdb=" O SER O 57 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.865A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.956A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.974A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.772A 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: 7.598A 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 66 through 67 removed outlier: 3.619A pdb=" N GLY K 67 " --> pdb=" O PHE K 58 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE K 58 " --> pdb=" O GLY K 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 125 through 126 Processing sheet with id=AB2, first strand: chain 'K' and resid 236 through 237 removed outlier: 3.813A pdb=" N GLN K 236 " --> pdb=" O GLY O 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 299 through 303 removed outlier: 3.743A pdb=" N THR K 299 " --> pdb=" O SER K 285 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER K 282 " --> pdb=" O HIS K 352 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 306 through 309 removed outlier: 6.292A pdb=" N LEU K 306 " --> pdb=" O GLN K 361 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LYS K 363 " --> pdb=" O LEU K 306 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU K 308 " --> pdb=" O LYS K 363 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR K 461 " --> pdb=" O LEU K 362 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL K 417 " --> pdb=" O TYR K 461 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU K 463 " --> pdb=" O GLY K 415 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY K 415 " --> pdb=" O LEU K 463 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR K 465 " --> pdb=" O LEU K 413 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU K 413 " --> pdb=" O TYR K 465 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE K 467 " --> pdb=" O TYR K 411 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR K 411 " --> pdb=" O ILE K 467 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLN K 469 " --> pdb=" O ILE K 409 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE K 409 " --> pdb=" O GLN K 469 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE K 414 " --> pdb=" O LYS K 433 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS K 432 " --> pdb=" O PHE K 440 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN K 438 " --> pdb=" O ILE K 434 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TRP K 439 " --> pdb=" O ILE K 450 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 365 through 367 Processing sheet with id=AB6, first strand: chain 'M' and resid 70 through 72 Processing sheet with id=AB7, first strand: chain 'O' and resid 12 through 16 removed outlier: 9.476A pdb=" N LEU O 67 " --> pdb=" O GLN O 2 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE O 4 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU O 69 " --> pdb=" O PHE O 4 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS O 6 " --> pdb=" O LEU O 69 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4421 1.34 - 1.45: 4827 1.45 - 1.57: 9157 1.57 - 1.69: 576 1.69 - 1.81: 82 Bond restraints: 19063 Sorted by residual: bond pdb=" C3' DC I -48 " pdb=" C2' DC I -48 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG I -40 " pdb=" C2' DG I -40 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.92e+00 bond pdb=" C3' DC I 0 " pdb=" C2' DC I 0 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.66e+00 bond pdb=" C3' DT I 1 " pdb=" C2' DT I 1 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.21e+00 ... (remaining 19058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 24802 1.07 - 2.15: 1660 2.15 - 3.22: 486 3.22 - 4.29: 25 4.29 - 5.36: 8 Bond angle restraints: 26981 Sorted by residual: angle pdb=" N3 DT J -23 " pdb=" C4 DT J -23 " pdb=" O4 DT J -23 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT J -50 " pdb=" C4 DT J -50 " pdb=" O4 DT J -50 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT J 69 " pdb=" C4 DT J 69 " pdb=" O4 DT J 69 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT J -67 " pdb=" C4 DT J -67 " pdb=" O4 DT J -67 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT J -39 " pdb=" C4 DT J -39 " pdb=" O4 DT J -39 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 26976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.07: 8858 24.07 - 48.15: 1302 48.15 - 72.22: 599 72.22 - 96.29: 8 96.29 - 120.36: 1 Dihedral angle restraints: 10768 sinusoidal: 6304 harmonic: 4464 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 -19.64 -120.36 1 3.50e+01 8.16e-04 1.18e+01 dihedral pdb=" CB MET D 56 " pdb=" CG MET D 56 " pdb=" SD MET D 56 " pdb=" CE MET D 56 " ideal model delta sinusoidal sigma weight residual -180.00 -124.37 -55.63 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CB MET H 56 " pdb=" CG MET H 56 " pdb=" SD MET H 56 " pdb=" CE MET H 56 " ideal model delta sinusoidal sigma weight residual -60.00 -110.16 50.16 3 1.50e+01 4.44e-03 8.87e+00 ... (remaining 10765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1645 0.028 - 0.055: 920 0.055 - 0.083: 297 0.083 - 0.110: 173 0.110 - 0.138: 25 Chirality restraints: 3060 Sorted by residual: chirality pdb=" C3' DC I -21 " pdb=" C4' DC I -21 " pdb=" O3' DC I -21 " pdb=" C2' DC I -21 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CB ILE K 409 " pdb=" CA ILE K 409 " pdb=" CG1 ILE K 409 " pdb=" CG2 ILE K 409 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE K 351 " pdb=" N ILE K 351 " pdb=" C ILE K 351 " pdb=" CB ILE K 351 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 3057 not shown) Planarity restraints: 2427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I -20 " -0.008 2.00e-02 2.50e+03 1.59e-02 5.72e+00 pdb=" N1 DC I -20 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DC I -20 " -0.037 2.00e-02 2.50e+03 pdb=" O2 DC I -20 " 0.022 2.00e-02 2.50e+03 pdb=" N3 DC I -20 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DC I -20 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC I -20 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DC I -20 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC I -20 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 42 " -0.016 2.00e-02 2.50e+03 7.88e-03 1.71e+00 pdb=" N9 DA J 42 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DA J 42 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA J 42 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA J 42 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA J 42 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA J 42 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DA J 42 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA J 42 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA J 42 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA J 42 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL K 35 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO K 36 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO K 36 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO K 36 " 0.016 5.00e-02 4.00e+02 ... (remaining 2424 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 522 2.69 - 3.24: 16222 3.24 - 3.79: 31699 3.79 - 4.35: 40360 4.35 - 4.90: 60105 Nonbonded interactions: 148908 Sorted by model distance: nonbonded pdb=" O2 DC I -46 " pdb=" N2 DG J 46 " model vdw 2.136 2.496 nonbonded pdb=" O2 DC I -51 " pdb=" N2 DG J 51 " model vdw 2.186 2.496 nonbonded pdb=" O2 DC I 19 " pdb=" N2 DG J -19 " model vdw 2.190 2.496 nonbonded pdb=" O VAL K 121 " pdb=" OG1 THR K 125 " model vdw 2.205 3.040 nonbonded pdb=" O ILE K 30 " pdb=" OG SER K 34 " model vdw 2.255 3.040 ... (remaining 148903 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 40 through 134) selection = (chain 'E' and resid 40 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 20.070 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 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 : 0.014 0.944 19090 Z= 0.562 Angle : 0.795 47.083 26994 Z= 0.559 Chirality : 0.041 0.138 3060 Planarity : 0.002 0.029 2427 Dihedral : 22.569 120.364 7876 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.07 % Allowed : 1.42 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.19), residues: 1498 helix: -0.43 (0.17), residues: 802 sheet: -1.23 (0.44), residues: 121 loop : -1.88 (0.21), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 67 TYR 0.019 0.001 TYR B 72 PHE 0.004 0.000 PHE L 88 TRP 0.002 0.000 TRP K 69 HIS 0.004 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.41 (19063) covalent geometry : angle 0.60911 / 0.55 (26981) hydrogen bonds : bond 0.17933 / 12.17 ( 994) hydrogen bonds : angle 5.99265 / 4.24 ( 2556) metal coordination : bond 0.35143 / 21.96 ( 27) metal coordination : angle 23.27464 / 14.38 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.6959 (m-30) cc_final: 0.6745 (m-30) REVERT: B 25 ASN cc_start: 0.7239 (m110) cc_final: 0.6843 (m110) REVERT: B 82 THR cc_start: 0.7842 (p) cc_final: 0.7636 (p) REVERT: B 84 MET cc_start: 0.6827 (mmm) cc_final: 0.6024 (mmm) REVERT: B 88 TYR cc_start: 0.7440 (m-10) cc_final: 0.7196 (m-80) REVERT: C 41 GLU cc_start: 0.8048 (tt0) cc_final: 0.7819 (tm-30) REVERT: C 43 VAL cc_start: 0.8735 (t) cc_final: 0.8454 (p) REVERT: C 99 ARG cc_start: 0.7083 (mmt180) cc_final: 0.6632 (mtt90) REVERT: D 32 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6237 (mt-10) REVERT: D 48 ASP cc_start: 0.8122 (m-30) cc_final: 0.7684 (p0) REVERT: D 105 LYS cc_start: 0.7824 (ttmt) cc_final: 0.7544 (tptt) REVERT: D 117 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7673 (mmtm) REVERT: E 59 GLU cc_start: 0.6822 (pp20) cc_final: 0.6237 (pp20) REVERT: E 76 GLN cc_start: 0.7157 (tt0) cc_final: 0.6828 (pt0) REVERT: F 43 VAL cc_start: 0.7911 (t) cc_final: 0.7488 (t) REVERT: F 49 LEU cc_start: 0.7029 (mt) cc_final: 0.5966 (mp) REVERT: F 74 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7314 (mt-10) REVERT: F 80 THR cc_start: 0.7317 (m) cc_final: 0.7063 (p) REVERT: G 99 ARG cc_start: 0.7837 (mpt180) cc_final: 0.7322 (mmp-170) REVERT: G 110 ASN cc_start: 0.8183 (t0) cc_final: 0.7719 (p0) REVERT: H 81 ASN cc_start: 0.5109 (m-40) cc_final: 0.4687 (m-40) REVERT: H 97 LEU cc_start: 0.7139 (mt) cc_final: 0.6927 (mt) REVERT: H 102 GLU cc_start: 0.6441 (mm-30) cc_final: 0.6113 (mm-30) REVERT: K 15 LYS cc_start: 0.7662 (tptp) cc_final: 0.7242 (mtpt) REVERT: K 59 MET cc_start: 0.6117 (ppp) cc_final: 0.5781 (ppp) REVERT: K 107 ASP cc_start: 0.7293 (p0) cc_final: 0.7026 (p0) REVERT: K 108 LEU cc_start: 0.7241 (tp) cc_final: 0.6938 (tp) REVERT: K 111 ASP cc_start: 0.4891 (t0) cc_final: 0.3841 (t0) REVERT: K 114 LEU cc_start: 0.7083 (mm) cc_final: 0.6720 (tt) REVERT: K 118 TRP cc_start: 0.4901 (t-100) cc_final: 0.3995 (t-100) REVERT: K 188 ASP cc_start: 0.7369 (m-30) cc_final: 0.6937 (t70) REVERT: K 228 GLN cc_start: 0.7445 (pp30) cc_final: 0.6305 (mp10) REVERT: K 229 ASN cc_start: 0.8380 (m110) cc_final: 0.7571 (t0) REVERT: K 297 LYS cc_start: 0.5481 (mtmt) cc_final: 0.5242 (mmtm) REVERT: K 301 ASP cc_start: 0.6854 (m-30) cc_final: 0.6366 (t0) REVERT: K 388 MET cc_start: 0.7675 (mmm) cc_final: 0.7266 (mmm) REVERT: K 389 LYS cc_start: 0.7745 (pttt) cc_final: 0.7476 (ttmt) REVERT: K 432 CYS cc_start: 0.6036 (t) cc_final: 0.5813 (m) REVERT: L 50 MET cc_start: 0.7193 (mmm) cc_final: 0.6977 (mmt) REVERT: L 57 ASN cc_start: 0.7133 (t0) cc_final: 0.6925 (t0) REVERT: M 30 ARG cc_start: 0.5527 (mtt-85) cc_final: 0.4900 (mmm160) REVERT: M 35 GLN cc_start: 0.7435 (tp40) cc_final: 0.7231 (tp-100) REVERT: M 75 ASN cc_start: 0.4682 (t0) cc_final: 0.4173 (t0) REVERT: M 95 ARG cc_start: 0.4543 (mtt180) cc_final: 0.3999 (mtp85) REVERT: N 32 TRP cc_start: 0.4096 (p-90) cc_final: 0.3819 (p-90) REVERT: N 45 GLN cc_start: 0.5447 (mm-40) cc_final: 0.5218 (mm-40) REVERT: N 80 LYS cc_start: 0.8173 (mttt) cc_final: 0.7856 (mmmt) REVERT: O 22 THR cc_start: 0.7445 (p) cc_final: 0.7108 (t) REVERT: O 36 ILE cc_start: 0.6262 (mt) cc_final: 0.6003 (mt) REVERT: O 61 ILE cc_start: 0.7835 (mt) cc_final: 0.7615 (mm) outliers start: 1 outliers final: 0 residues processed: 474 average time/residue: 0.1744 time to fit residues: 117.2180 Evaluate side-chains 293 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 92 GLN F 64 ASN F 93 GLN G 24 GLN H 64 ASN K 53 ASN K 70 ASN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 229 ASN K 459 GLN K 469 GLN K 471 ASN L 51 ASN O 2 GLN O 41 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.098080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.073548 restraints weight = 51052.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.073662 restraints weight = 31098.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.074258 restraints weight = 23008.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.074468 restraints weight = 20907.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.074482 restraints weight = 18794.286| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 19090 Z= 0.322 Angle : 0.842 11.740 26994 Z= 0.454 Chirality : 0.052 0.248 3060 Planarity : 0.006 0.064 2427 Dihedral : 28.203 116.906 4833 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.73 % Allowed : 12.44 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1498 helix: 0.46 (0.17), residues: 827 sheet: -0.67 (0.48), residues: 116 loop : -1.78 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 45 TYR 0.025 0.003 TYR K 461 PHE 0.041 0.003 PHE K 11 TRP 0.011 0.002 TRP K 242 HIS 0.020 0.003 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.32 (19063) covalent geometry : angle 0.83368 / 0.45 (26981) hydrogen bonds : bond 0.08680 / 6.01 ( 994) hydrogen bonds : angle 4.34185 / 3.12 ( 2556) metal coordination : bond 0.03347 / 2.30 ( 27) metal coordination : angle 5.54451 / 3.38 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 276 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: A 106 ASP cc_start: 0.7725 (m-30) cc_final: 0.7492 (m-30) REVERT: A 120 MET cc_start: 0.8287 (mmt) cc_final: 0.7972 (mmt) REVERT: D 73 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8188 (tp30) REVERT: D 88 SER cc_start: 0.9291 (m) cc_final: 0.8926 (p) REVERT: E 59 GLU cc_start: 0.8385 (pp20) cc_final: 0.8017 (pp20) REVERT: F 80 THR cc_start: 0.9309 (m) cc_final: 0.8825 (p) REVERT: F 85 ASP cc_start: 0.8702 (m-30) cc_final: 0.8385 (m-30) REVERT: H 59 MET cc_start: 0.8912 (mmm) cc_final: 0.8475 (mmt) REVERT: K 15 LYS cc_start: 0.8094 (tptp) cc_final: 0.7224 (mtpt) REVERT: K 111 ASP cc_start: 0.7136 (t0) cc_final: 0.6205 (t0) REVERT: K 118 TRP cc_start: 0.7520 (t-100) cc_final: 0.6482 (t-100) REVERT: K 126 MET cc_start: 0.7352 (ptp) cc_final: 0.6963 (ptp) REVERT: K 142 MET cc_start: 0.7748 (mpp) cc_final: 0.6832 (mtt) REVERT: K 388 MET cc_start: 0.7915 (mmm) cc_final: 0.7424 (mmm) REVERT: L 7 GLN cc_start: 0.6209 (tm-30) cc_final: 0.5644 (tt0) REVERT: L 33 LEU cc_start: 0.8099 (mt) cc_final: 0.7802 (mt) REVERT: M 30 ARG cc_start: 0.6261 (mtt-85) cc_final: 0.5913 (mmm160) REVERT: M 35 GLN cc_start: 0.8179 (tp40) cc_final: 0.7765 (tp-100) REVERT: N 80 LYS cc_start: 0.9047 (mttt) cc_final: 0.8339 (mmmt) REVERT: O 29 LYS cc_start: 0.7102 (mttm) cc_final: 0.6854 (mmtp) REVERT: O 45 PHE cc_start: 0.8453 (t80) cc_final: 0.8196 (t80) REVERT: O 64 GLU cc_start: 0.7749 (mp0) cc_final: 0.7340 (mp0) outliers start: 50 outliers final: 32 residues processed: 305 average time/residue: 0.1561 time to fit residues: 69.5695 Evaluate side-chains 263 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 50 HIS Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 8 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 62 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 156 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 132 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.099886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.074304 restraints weight = 50593.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.076047 restraints weight = 27587.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077408 restraints weight = 16967.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.077197 restraints weight = 14375.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.077298 restraints weight = 13942.924| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 19090 Z= 0.157 Angle : 0.614 13.574 26994 Z= 0.343 Chirality : 0.043 0.291 3060 Planarity : 0.004 0.043 2427 Dihedral : 28.023 118.211 4833 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.53 % Allowed : 14.53 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1498 helix: 1.29 (0.18), residues: 826 sheet: -0.40 (0.49), residues: 115 loop : -1.51 (0.23), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 468 TYR 0.023 0.001 TYR K 117 PHE 0.015 0.001 PHE K 40 TRP 0.014 0.002 TRP K 118 HIS 0.006 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (19063) covalent geometry : angle 0.59783 / 0.34 (26981) hydrogen bonds : bond 0.06722 / 4.68 ( 994) hydrogen bonds : angle 3.85341 / 2.77 ( 2556) metal coordination : bond 0.02211 / 1.31 ( 27) metal coordination : angle 6.48460 / 4.05 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7773 (m-30) cc_final: 0.7506 (m-30) REVERT: A 108 ASN cc_start: 0.9206 (t0) cc_final: 0.8928 (t0) REVERT: A 120 MET cc_start: 0.8087 (mmt) cc_final: 0.7732 (mmt) REVERT: B 63 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7852 (mt-10) REVERT: C 56 GLU cc_start: 0.8033 (tt0) cc_final: 0.7749 (tt0) REVERT: D 88 SER cc_start: 0.9259 (m) cc_final: 0.8891 (p) REVERT: D 98 LEU cc_start: 0.9288 (mt) cc_final: 0.8952 (mm) REVERT: E 59 GLU cc_start: 0.8281 (pp20) cc_final: 0.7884 (pp20) REVERT: E 106 ASP cc_start: 0.7323 (m-30) cc_final: 0.6875 (m-30) REVERT: F 80 THR cc_start: 0.9260 (m) cc_final: 0.8826 (p) REVERT: G 90 ASP cc_start: 0.8807 (t0) cc_final: 0.8177 (t0) REVERT: H 59 MET cc_start: 0.8898 (mmm) cc_final: 0.8509 (mmt) REVERT: K 15 LYS cc_start: 0.7992 (tptp) cc_final: 0.7166 (mtpt) REVERT: K 111 ASP cc_start: 0.6999 (t0) cc_final: 0.6198 (t0) REVERT: K 142 MET cc_start: 0.7735 (mpp) cc_final: 0.7112 (mtt) REVERT: K 228 GLN cc_start: 0.7428 (pp30) cc_final: 0.6590 (mp10) REVERT: K 388 MET cc_start: 0.8085 (mmm) cc_final: 0.7573 (mmm) REVERT: L 50 MET cc_start: 0.8117 (mmt) cc_final: 0.7905 (mmt) REVERT: M 30 ARG cc_start: 0.6285 (mtt-85) cc_final: 0.5841 (mmm160) REVERT: M 35 GLN cc_start: 0.8065 (tp40) cc_final: 0.7531 (tp-100) REVERT: M 95 ARG cc_start: 0.6289 (mtp-110) cc_final: 0.5677 (mtm110) REVERT: N 67 ASP cc_start: 0.8567 (t0) cc_final: 0.8362 (t0) REVERT: N 80 LYS cc_start: 0.8960 (mttt) cc_final: 0.8314 (mmmt) REVERT: N 85 LEU cc_start: 0.8081 (mt) cc_final: 0.7763 (mp) REVERT: O 29 LYS cc_start: 0.7279 (mttm) cc_final: 0.7068 (mmtp) REVERT: O 45 PHE cc_start: 0.8379 (t80) cc_final: 0.8143 (t80) outliers start: 34 outliers final: 22 residues processed: 273 average time/residue: 0.1531 time to fit residues: 62.1277 Evaluate side-chains 250 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain O residue 8 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 153 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 367 HIS M 34 GLN M 72 HIS O 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.098929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.074216 restraints weight = 50834.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.075199 restraints weight = 26363.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.075848 restraints weight = 17593.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076150 restraints weight = 15934.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076173 restraints weight = 14105.713| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19090 Z= 0.163 Angle : 0.608 10.189 26994 Z= 0.339 Chirality : 0.043 0.202 3060 Planarity : 0.004 0.034 2427 Dihedral : 28.150 120.796 4833 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.35 % Allowed : 14.46 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.22), residues: 1498 helix: 1.54 (0.19), residues: 820 sheet: -0.28 (0.50), residues: 115 loop : -1.50 (0.23), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 99 TYR 0.027 0.002 TYR B 88 PHE 0.012 0.001 PHE K 216 TRP 0.013 0.002 TRP K 118 HIS 0.007 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (19063) covalent geometry : angle 0.59616 / 0.34 (26981) hydrogen bonds : bond 0.06527 / 4.53 ( 994) hydrogen bonds : angle 3.75340 / 2.71 ( 2556) metal coordination : bond 0.01644 / 1.03 ( 27) metal coordination : angle 5.40091 / 3.38 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7791 (m-30) cc_final: 0.7501 (m-30) REVERT: D 88 SER cc_start: 0.9221 (m) cc_final: 0.8922 (p) REVERT: D 98 LEU cc_start: 0.9206 (mt) cc_final: 0.8926 (mm) REVERT: E 59 GLU cc_start: 0.8263 (pp20) cc_final: 0.7901 (pp20) REVERT: F 80 THR cc_start: 0.9317 (m) cc_final: 0.8868 (p) REVERT: F 85 ASP cc_start: 0.8544 (m-30) cc_final: 0.8210 (m-30) REVERT: G 90 ASP cc_start: 0.8787 (t0) cc_final: 0.8240 (t0) REVERT: H 80 TYR cc_start: 0.7872 (m-80) cc_final: 0.7381 (m-80) REVERT: K 15 LYS cc_start: 0.7943 (tptp) cc_final: 0.7045 (mtpt) REVERT: K 111 ASP cc_start: 0.7100 (t0) cc_final: 0.6474 (t0) REVERT: K 114 LEU cc_start: 0.7306 (tp) cc_final: 0.7098 (tt) REVERT: K 142 MET cc_start: 0.7749 (mpp) cc_final: 0.7162 (mtt) REVERT: K 166 MET cc_start: 0.7759 (mtt) cc_final: 0.7380 (mmm) REVERT: K 228 GLN cc_start: 0.7403 (pp30) cc_final: 0.6464 (mp10) REVERT: K 388 MET cc_start: 0.8108 (mmm) cc_final: 0.7620 (mmm) REVERT: L 38 TRP cc_start: 0.8938 (t60) cc_final: 0.8703 (t60) REVERT: M 30 ARG cc_start: 0.6313 (mtt-85) cc_final: 0.5759 (mmm160) REVERT: M 35 GLN cc_start: 0.8081 (tp40) cc_final: 0.7738 (tp-100) REVERT: M 95 ARG cc_start: 0.6463 (mtp-110) cc_final: 0.5854 (mtm110) REVERT: N 67 ASP cc_start: 0.8682 (t0) cc_final: 0.8399 (t0) REVERT: N 85 LEU cc_start: 0.8238 (mt) cc_final: 0.8002 (mp) REVERT: O 45 PHE cc_start: 0.8396 (t80) cc_final: 0.8140 (t80) REVERT: O 64 GLU cc_start: 0.7455 (mp0) cc_final: 0.7224 (mp0) outliers start: 45 outliers final: 34 residues processed: 262 average time/residue: 0.1478 time to fit residues: 58.3282 Evaluate side-chains 259 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 432 CYS Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 79 ASP Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 81 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 131 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN K 70 ASN ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN M 64 GLN M 72 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.098740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.074261 restraints weight = 50987.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074904 restraints weight = 28028.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.075545 restraints weight = 19522.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.075711 restraints weight = 16560.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.075920 restraints weight = 15435.309| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19090 Z= 0.149 Angle : 0.592 9.807 26994 Z= 0.331 Chirality : 0.042 0.197 3060 Planarity : 0.003 0.033 2427 Dihedral : 28.176 121.945 4833 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.35 % Allowed : 15.20 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1498 helix: 1.67 (0.19), residues: 819 sheet: -0.17 (0.50), residues: 115 loop : -1.38 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 99 TYR 0.016 0.001 TYR B 88 PHE 0.041 0.001 PHE K 11 TRP 0.007 0.001 TRP K 118 HIS 0.005 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (19063) covalent geometry : angle 0.58170 / 0.33 (26981) hydrogen bonds : bond 0.06277 / 4.36 ( 994) hydrogen bonds : angle 3.64534 / 2.63 ( 2556) metal coordination : bond 0.01544 / 0.94 ( 27) metal coordination : angle 5.12989 / 3.26 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7715 (m-30) cc_final: 0.7428 (m-30) REVERT: D 88 SER cc_start: 0.9236 (m) cc_final: 0.8936 (p) REVERT: D 98 LEU cc_start: 0.9201 (mt) cc_final: 0.8908 (mm) REVERT: E 59 GLU cc_start: 0.8246 (pp20) cc_final: 0.7915 (pp20) REVERT: E 106 ASP cc_start: 0.7299 (m-30) cc_final: 0.6904 (m-30) REVERT: F 80 THR cc_start: 0.9294 (m) cc_final: 0.8852 (p) REVERT: G 90 ASP cc_start: 0.8789 (t0) cc_final: 0.8361 (t0) REVERT: H 30 ARG cc_start: 0.8264 (mtp85) cc_final: 0.8057 (ttm-80) REVERT: H 59 MET cc_start: 0.8651 (mmm) cc_final: 0.8392 (mmm) REVERT: K 15 LYS cc_start: 0.8017 (tptp) cc_final: 0.7012 (mtpt) REVERT: K 111 ASP cc_start: 0.7122 (t0) cc_final: 0.6418 (t0) REVERT: K 114 LEU cc_start: 0.7238 (tp) cc_final: 0.6937 (tt) REVERT: K 142 MET cc_start: 0.7757 (mpp) cc_final: 0.7099 (mtt) REVERT: K 228 GLN cc_start: 0.7434 (pp30) cc_final: 0.6477 (mp10) REVERT: K 388 MET cc_start: 0.8086 (mmm) cc_final: 0.7615 (mmm) REVERT: M 30 ARG cc_start: 0.6476 (mtt-85) cc_final: 0.5945 (mmm160) REVERT: M 35 GLN cc_start: 0.8125 (tp40) cc_final: 0.7780 (tp-100) REVERT: N 67 ASP cc_start: 0.8710 (t0) cc_final: 0.8373 (t0) REVERT: N 85 LEU cc_start: 0.8225 (mt) cc_final: 0.8008 (mp) REVERT: O 45 PHE cc_start: 0.8409 (t80) cc_final: 0.8138 (t80) REVERT: O 64 GLU cc_start: 0.7711 (mp0) cc_final: 0.7476 (mp0) outliers start: 45 outliers final: 36 residues processed: 260 average time/residue: 0.1490 time to fit residues: 57.9608 Evaluate side-chains 256 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 432 CYS Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 79 ASP Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 8 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 24 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 120 optimal weight: 0.0970 chunk 55 optimal weight: 0.5980 chunk 102 optimal weight: 0.0470 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 131 optimal weight: 0.0170 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN M 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.099392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.074710 restraints weight = 51536.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075541 restraints weight = 30097.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.076581 restraints weight = 19537.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.076893 restraints weight = 15680.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.076957 restraints weight = 14481.670| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19090 Z= 0.125 Angle : 0.563 8.579 26994 Z= 0.318 Chirality : 0.041 0.200 3060 Planarity : 0.003 0.048 2427 Dihedral : 28.121 123.787 4833 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.61 % Allowed : 16.32 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1498 helix: 1.89 (0.19), residues: 811 sheet: -0.06 (0.52), residues: 105 loop : -1.31 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 468 TYR 0.020 0.001 TYR M 49 PHE 0.032 0.001 PHE K 11 TRP 0.006 0.001 TRP K 242 HIS 0.005 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.12 (19063) covalent geometry : angle 0.55424 / 0.32 (26981) hydrogen bonds : bond 0.05748 / 4.03 ( 994) hydrogen bonds : angle 3.50685 / 2.53 ( 2556) metal coordination : bond 0.01482 / 0.85 ( 27) metal coordination : angle 4.59308 / 2.92 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7672 (m-30) cc_final: 0.7259 (m-30) REVERT: D 88 SER cc_start: 0.9227 (m) cc_final: 0.8939 (p) REVERT: D 98 LEU cc_start: 0.9158 (mt) cc_final: 0.8840 (mm) REVERT: E 59 GLU cc_start: 0.8167 (pp20) cc_final: 0.7855 (pp20) REVERT: E 106 ASP cc_start: 0.7122 (m-30) cc_final: 0.6808 (m-30) REVERT: F 80 THR cc_start: 0.9280 (m) cc_final: 0.8862 (p) REVERT: G 90 ASP cc_start: 0.8766 (t0) cc_final: 0.8361 (t0) REVERT: H 59 MET cc_start: 0.8698 (mmm) cc_final: 0.8286 (mmt) REVERT: K 15 LYS cc_start: 0.8114 (tptp) cc_final: 0.7135 (mtpt) REVERT: K 111 ASP cc_start: 0.7127 (t0) cc_final: 0.6466 (t0) REVERT: K 114 LEU cc_start: 0.7234 (tp) cc_final: 0.6991 (tt) REVERT: K 142 MET cc_start: 0.7700 (mpp) cc_final: 0.7071 (mtt) REVERT: K 228 GLN cc_start: 0.7429 (pp30) cc_final: 0.6507 (mp10) REVERT: K 388 MET cc_start: 0.8052 (mmm) cc_final: 0.7587 (mmm) REVERT: M 18 ASN cc_start: 0.7079 (OUTLIER) cc_final: 0.6620 (t0) REVERT: M 30 ARG cc_start: 0.6377 (mtt-85) cc_final: 0.5682 (mmm160) REVERT: M 31 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7379 (mm-30) REVERT: M 35 GLN cc_start: 0.8204 (tp40) cc_final: 0.7833 (tp-100) REVERT: M 45 LEU cc_start: 0.7685 (tp) cc_final: 0.7413 (tt) REVERT: N 67 ASP cc_start: 0.8636 (t0) cc_final: 0.8237 (t0) REVERT: O 45 PHE cc_start: 0.8394 (t80) cc_final: 0.8103 (t80) REVERT: O 64 GLU cc_start: 0.7638 (mp0) cc_final: 0.7390 (mp0) outliers start: 35 outliers final: 30 residues processed: 256 average time/residue: 0.1488 time to fit residues: 57.0282 Evaluate side-chains 259 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 432 CYS Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 79 ASP Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 83 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 127 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN D 44 GLN ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 HIS ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN M 72 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.096011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.071197 restraints weight = 50552.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.071753 restraints weight = 30053.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.072313 restraints weight = 21594.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.072564 restraints weight = 18136.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.072727 restraints weight = 16952.141| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19090 Z= 0.240 Angle : 0.715 9.393 26994 Z= 0.382 Chirality : 0.047 0.211 3060 Planarity : 0.005 0.060 2427 Dihedral : 28.506 125.170 4833 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.43 % Allowed : 16.32 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.22), residues: 1498 helix: 1.50 (0.18), residues: 818 sheet: -0.48 (0.45), residues: 133 loop : -1.27 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG H 30 TYR 0.021 0.002 TYR K 461 PHE 0.034 0.002 PHE K 11 TRP 0.011 0.002 TRP K 242 HIS 0.006 0.001 HIS K 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.24 (19063) covalent geometry : angle 0.70655 / 0.38 (26981) hydrogen bonds : bond 0.07551 / 5.16 ( 994) hydrogen bonds : angle 3.82994 / 2.76 ( 2556) metal coordination : bond 0.01519 / 0.93 ( 27) metal coordination : angle 4.99264 / 3.20 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7573 (m-30) cc_final: 0.7345 (m-30) REVERT: A 120 MET cc_start: 0.8169 (mmt) cc_final: 0.7808 (mmt) REVERT: B 63 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7988 (mt-10) REVERT: D 88 SER cc_start: 0.9161 (m) cc_final: 0.8922 (p) REVERT: D 98 LEU cc_start: 0.9194 (mt) cc_final: 0.8832 (mm) REVERT: E 59 GLU cc_start: 0.8313 (pp20) cc_final: 0.7957 (pp20) REVERT: E 106 ASP cc_start: 0.7266 (m-30) cc_final: 0.6982 (m-30) REVERT: F 80 THR cc_start: 0.9297 (m) cc_final: 0.8782 (p) REVERT: F 85 ASP cc_start: 0.8624 (m-30) cc_final: 0.8306 (m-30) REVERT: G 76 THR cc_start: 0.8818 (m) cc_final: 0.8452 (p) REVERT: G 90 ASP cc_start: 0.8829 (t0) cc_final: 0.8384 (t0) REVERT: H 59 MET cc_start: 0.8871 (mmm) cc_final: 0.8565 (mmm) REVERT: K 15 LYS cc_start: 0.7972 (tptp) cc_final: 0.7067 (mtpt) REVERT: K 111 ASP cc_start: 0.7310 (t0) cc_final: 0.6427 (t0) REVERT: K 114 LEU cc_start: 0.7360 (tp) cc_final: 0.7118 (tt) REVERT: K 142 MET cc_start: 0.7843 (mpp) cc_final: 0.7283 (mtt) REVERT: K 388 MET cc_start: 0.8087 (mmm) cc_final: 0.7595 (mmm) REVERT: L 84 GLN cc_start: 0.8019 (mt0) cc_final: 0.7615 (mp10) REVERT: M 18 ASN cc_start: 0.7240 (OUTLIER) cc_final: 0.6838 (t0) REVERT: M 30 ARG cc_start: 0.6492 (mtt-85) cc_final: 0.6129 (mmm160) REVERT: M 35 GLN cc_start: 0.8296 (tp40) cc_final: 0.7827 (tp-100) REVERT: N 67 ASP cc_start: 0.8689 (t0) cc_final: 0.8289 (t0) REVERT: N 85 LEU cc_start: 0.8177 (mt) cc_final: 0.7961 (mp) REVERT: O 45 PHE cc_start: 0.8345 (t80) cc_final: 0.8083 (t80) REVERT: O 64 GLU cc_start: 0.7708 (mp0) cc_final: 0.7447 (mp0) outliers start: 46 outliers final: 35 residues processed: 260 average time/residue: 0.1404 time to fit residues: 55.2586 Evaluate side-chains 254 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 59 MET Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 432 CYS Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 8 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 45 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 87 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 119 optimal weight: 0.0270 chunk 2 optimal weight: 0.0970 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN M 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.098050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.073084 restraints weight = 51192.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.073917 restraints weight = 29275.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.074556 restraints weight = 19790.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.074673 restraints weight = 17093.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074983 restraints weight = 15951.776| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19090 Z= 0.132 Angle : 0.600 8.483 26994 Z= 0.334 Chirality : 0.042 0.205 3060 Planarity : 0.004 0.055 2427 Dihedral : 28.258 127.803 4833 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.46 % Allowed : 17.88 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.22), residues: 1498 helix: 1.88 (0.19), residues: 811 sheet: -0.25 (0.48), residues: 115 loop : -1.24 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 468 TYR 0.028 0.001 TYR H 80 PHE 0.010 0.001 PHE H 67 TRP 0.005 0.001 TRP L 38 HIS 0.005 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (19063) covalent geometry : angle 0.59184 / 0.33 (26981) hydrogen bonds : bond 0.06007 / 4.19 ( 994) hydrogen bonds : angle 3.56166 / 2.55 ( 2556) metal coordination : bond 0.01445 / 0.81 ( 27) metal coordination : angle 4.59346 / 2.94 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 0.566 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 106 ASP cc_start: 0.7557 (m-30) cc_final: 0.7311 (m-30) REVERT: A 108 ASN cc_start: 0.9293 (t0) cc_final: 0.9048 (t0) REVERT: A 120 MET cc_start: 0.8089 (mmt) cc_final: 0.7711 (mmt) REVERT: D 88 SER cc_start: 0.9218 (m) cc_final: 0.8923 (p) REVERT: D 98 LEU cc_start: 0.9168 (mt) cc_final: 0.8872 (mm) REVERT: E 59 GLU cc_start: 0.8192 (pp20) cc_final: 0.7864 (pp20) REVERT: E 106 ASP cc_start: 0.7139 (m-30) cc_final: 0.6842 (m-30) REVERT: F 80 THR cc_start: 0.9312 (m) cc_final: 0.8831 (p) REVERT: F 85 ASP cc_start: 0.8503 (m-30) cc_final: 0.8214 (m-30) REVERT: G 90 ASP cc_start: 0.8619 (t0) cc_final: 0.8280 (t0) REVERT: H 59 MET cc_start: 0.8737 (mmm) cc_final: 0.8385 (mmm) REVERT: K 15 LYS cc_start: 0.8125 (tptp) cc_final: 0.7135 (mtpt) REVERT: K 111 ASP cc_start: 0.7295 (t0) cc_final: 0.6531 (t0) REVERT: K 114 LEU cc_start: 0.7431 (tp) cc_final: 0.7120 (tt) REVERT: K 142 MET cc_start: 0.7712 (mpp) cc_final: 0.7176 (mtt) REVERT: K 388 MET cc_start: 0.8037 (mmm) cc_final: 0.7547 (mmm) REVERT: L 84 GLN cc_start: 0.7811 (mt0) cc_final: 0.7399 (mp10) REVERT: M 18 ASN cc_start: 0.7214 (OUTLIER) cc_final: 0.6778 (t0) REVERT: M 30 ARG cc_start: 0.6376 (mtt-85) cc_final: 0.5826 (mmm160) REVERT: M 31 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7258 (mm-30) REVERT: M 35 GLN cc_start: 0.8246 (tp40) cc_final: 0.7900 (tp-100) REVERT: N 52 GLU cc_start: 0.7753 (mp0) cc_final: 0.7533 (mp0) REVERT: N 67 ASP cc_start: 0.8677 (t0) cc_final: 0.8273 (t0) REVERT: O 45 PHE cc_start: 0.8391 (t80) cc_final: 0.8121 (t80) REVERT: O 64 GLU cc_start: 0.7713 (mp0) cc_final: 0.7429 (mp0) outliers start: 33 outliers final: 27 residues processed: 266 average time/residue: 0.1393 time to fit residues: 56.1149 Evaluate side-chains 260 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 432 CYS Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain N residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 12 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.097405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.072348 restraints weight = 50967.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.073148 restraints weight = 29189.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.073746 restraints weight = 20101.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073870 restraints weight = 17294.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074067 restraints weight = 16234.715| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19090 Z= 0.158 Angle : 0.627 8.184 26994 Z= 0.347 Chirality : 0.043 0.211 3060 Planarity : 0.004 0.058 2427 Dihedral : 28.340 130.030 4833 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.38 % Allowed : 18.41 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.22), residues: 1498 helix: 1.77 (0.19), residues: 816 sheet: -0.41 (0.45), residues: 135 loop : -1.17 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 468 TYR 0.042 0.002 TYR H 80 PHE 0.011 0.001 PHE K 216 TRP 0.008 0.001 TRP L 38 HIS 0.005 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (19063) covalent geometry : angle 0.61916 / 0.35 (26981) hydrogen bonds : bond 0.06252 / 4.31 ( 994) hydrogen bonds : angle 3.61488 / 2.59 ( 2556) metal coordination : bond 0.01461 / 0.82 ( 27) metal coordination : angle 4.44732 / 2.84 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7565 (m-30) cc_final: 0.7328 (m-30) REVERT: A 108 ASN cc_start: 0.9260 (t0) cc_final: 0.9013 (t0) REVERT: B 63 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7956 (mt-10) REVERT: D 88 SER cc_start: 0.9145 (m) cc_final: 0.8942 (p) REVERT: D 98 LEU cc_start: 0.9179 (mt) cc_final: 0.8880 (mm) REVERT: D 113 LYS cc_start: 0.9010 (ttmm) cc_final: 0.8613 (tttp) REVERT: E 59 GLU cc_start: 0.8278 (pp20) cc_final: 0.8061 (pt0) REVERT: E 106 ASP cc_start: 0.7128 (m-30) cc_final: 0.6824 (m-30) REVERT: F 80 THR cc_start: 0.9290 (m) cc_final: 0.8804 (p) REVERT: F 85 ASP cc_start: 0.8529 (m-30) cc_final: 0.8157 (m-30) REVERT: G 90 ASP cc_start: 0.8616 (t0) cc_final: 0.8359 (t0) REVERT: H 59 MET cc_start: 0.8770 (mmm) cc_final: 0.8237 (mmt) REVERT: H 79 HIS cc_start: 0.7709 (m-70) cc_final: 0.7408 (m-70) REVERT: K 15 LYS cc_start: 0.8114 (tptp) cc_final: 0.7124 (mtpt) REVERT: K 111 ASP cc_start: 0.7318 (t0) cc_final: 0.6556 (t0) REVERT: K 114 LEU cc_start: 0.7476 (tp) cc_final: 0.7166 (tt) REVERT: K 142 MET cc_start: 0.7842 (mpp) cc_final: 0.7291 (mtt) REVERT: K 388 MET cc_start: 0.8037 (mmm) cc_final: 0.7514 (mmm) REVERT: L 84 GLN cc_start: 0.7825 (mt0) cc_final: 0.7411 (mp10) REVERT: M 18 ASN cc_start: 0.7189 (OUTLIER) cc_final: 0.6717 (t0) REVERT: M 30 ARG cc_start: 0.6371 (mtt-85) cc_final: 0.5848 (mmm160) REVERT: M 31 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7244 (mm-30) REVERT: M 35 GLN cc_start: 0.8263 (tp40) cc_final: 0.7995 (tp-100) REVERT: M 44 ASP cc_start: 0.7610 (t70) cc_final: 0.7222 (t70) REVERT: N 52 GLU cc_start: 0.7747 (mp0) cc_final: 0.7519 (mp0) REVERT: N 67 ASP cc_start: 0.8687 (t0) cc_final: 0.8291 (t0) REVERT: O 45 PHE cc_start: 0.8344 (t80) cc_final: 0.8054 (t80) REVERT: O 64 GLU cc_start: 0.7675 (mp0) cc_final: 0.7369 (mp0) outliers start: 32 outliers final: 27 residues processed: 256 average time/residue: 0.1470 time to fit residues: 56.9377 Evaluate side-chains 257 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 432 CYS Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 127 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 136 optimal weight: 0.0050 chunk 113 optimal weight: 0.5980 chunk 65 optimal weight: 0.4980 chunk 168 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.097841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.073241 restraints weight = 51051.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073723 restraints weight = 31229.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.074520 restraints weight = 21114.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.074976 restraints weight = 16934.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.075017 restraints weight = 15691.065| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19090 Z= 0.136 Angle : 0.608 8.673 26994 Z= 0.338 Chirality : 0.042 0.211 3060 Planarity : 0.004 0.052 2427 Dihedral : 28.291 131.712 4833 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.38 % Allowed : 18.70 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.22), residues: 1498 helix: 1.83 (0.19), residues: 817 sheet: -0.36 (0.45), residues: 134 loop : -1.17 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 468 TYR 0.022 0.002 TYR L 15 PHE 0.054 0.001 PHE L 88 TRP 0.006 0.001 TRP K 242 HIS 0.005 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (19063) covalent geometry : angle 0.60075 / 0.34 (26981) hydrogen bonds : bond 0.05899 / 4.10 ( 994) hydrogen bonds : angle 3.55028 / 2.54 ( 2556) metal coordination : bond 0.01465 / 0.78 ( 27) metal coordination : angle 4.21194 / 2.68 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7557 (m-30) cc_final: 0.7311 (m-30) REVERT: A 108 ASN cc_start: 0.9247 (t0) cc_final: 0.9005 (t0) REVERT: A 120 MET cc_start: 0.8119 (mmt) cc_final: 0.7740 (mmt) REVERT: B 63 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7961 (mt-10) REVERT: D 98 LEU cc_start: 0.9162 (mt) cc_final: 0.8870 (mm) REVERT: D 113 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8581 (tttp) REVERT: E 59 GLU cc_start: 0.8246 (pp20) cc_final: 0.8042 (pt0) REVERT: E 106 ASP cc_start: 0.7115 (m-30) cc_final: 0.6836 (m-30) REVERT: F 80 THR cc_start: 0.9278 (m) cc_final: 0.8809 (p) REVERT: F 85 ASP cc_start: 0.8537 (m-30) cc_final: 0.8191 (m-30) REVERT: F 88 TYR cc_start: 0.8138 (m-80) cc_final: 0.7657 (m-10) REVERT: G 90 ASP cc_start: 0.8571 (t0) cc_final: 0.8323 (t0) REVERT: H 59 MET cc_start: 0.8829 (mmm) cc_final: 0.8339 (mmt) REVERT: H 79 HIS cc_start: 0.7560 (m-70) cc_final: 0.7239 (m-70) REVERT: H 80 TYR cc_start: 0.7458 (m-80) cc_final: 0.6216 (m-80) REVERT: K 15 LYS cc_start: 0.8092 (tptp) cc_final: 0.7108 (mtpt) REVERT: K 111 ASP cc_start: 0.7314 (t0) cc_final: 0.6538 (t0) REVERT: K 114 LEU cc_start: 0.7533 (tp) cc_final: 0.7226 (tt) REVERT: K 142 MET cc_start: 0.7835 (mpp) cc_final: 0.7293 (mtt) REVERT: K 388 MET cc_start: 0.8024 (mmm) cc_final: 0.7481 (mmm) REVERT: L 84 GLN cc_start: 0.7909 (mt0) cc_final: 0.7487 (mp10) REVERT: M 18 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.6678 (t0) REVERT: M 30 ARG cc_start: 0.6325 (mtt-85) cc_final: 0.5827 (mmm160) REVERT: M 35 GLN cc_start: 0.8246 (tp40) cc_final: 0.7992 (tp-100) REVERT: M 44 ASP cc_start: 0.7584 (t70) cc_final: 0.7300 (t70) REVERT: N 52 GLU cc_start: 0.7716 (mp0) cc_final: 0.7499 (mp0) REVERT: N 67 ASP cc_start: 0.8678 (t0) cc_final: 0.8302 (t0) REVERT: O 45 PHE cc_start: 0.8304 (t80) cc_final: 0.8033 (t80) REVERT: O 64 GLU cc_start: 0.7663 (mp0) cc_final: 0.7423 (mp0) REVERT: O 72 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.8157 (mmm-85) outliers start: 32 outliers final: 28 residues processed: 256 average time/residue: 0.1418 time to fit residues: 55.3717 Evaluate side-chains 259 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 432 CYS Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.0040 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.097645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.072573 restraints weight = 51191.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.073577 restraints weight = 28123.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.074065 restraints weight = 18354.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.074379 restraints weight = 16443.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.074411 restraints weight = 14848.457| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19090 Z= 0.142 Angle : 0.605 8.423 26994 Z= 0.336 Chirality : 0.042 0.211 3060 Planarity : 0.004 0.048 2427 Dihedral : 28.311 133.516 4833 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.38 % Allowed : 18.78 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.22), residues: 1498 helix: 1.78 (0.19), residues: 823 sheet: -0.34 (0.45), residues: 134 loop : -1.12 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 468 TYR 0.023 0.002 TYR D 80 PHE 0.046 0.001 PHE L 88 TRP 0.007 0.001 TRP K 242 HIS 0.005 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (19063) covalent geometry : angle 0.59905 / 0.34 (26981) hydrogen bonds : bond 0.05951 / 4.13 ( 994) hydrogen bonds : angle 3.54699 / 2.54 ( 2556) metal coordination : bond 0.01498 / 0.80 ( 27) metal coordination : angle 3.98956 / 2.53 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3072.17 seconds wall clock time: 53 minutes 45.31 seconds (3225.31 seconds total)