Starting phenix.real_space_refine on Sat Sep 28 03:02:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9l_10415/09_2024/6t9l_10415.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9l_10415/09_2024/6t9l_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9l_10415/09_2024/6t9l_10415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9l_10415/09_2024/6t9l_10415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9l_10415/09_2024/6t9l_10415.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9l_10415/09_2024/6t9l_10415.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 10.92, per 1000 atoms: 0.60 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: 4.30 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 7.51 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: 8.09 Time building geometry restraints manager: 5.09 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' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 9.77e-01 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.451 -0.029 3.00e-02 1.11e+03 9.44e-01 bond pdb=" N PRO G 109 " pdb=" CA PRO G 109 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 8.72e-01 bond pdb=" O4' DC I -20 " pdb=" C1' DC I -20 " ideal model delta sigma weight residual 1.414 1.396 0.018 2.00e-02 2.50e+03 8.15e-01 bond pdb=" C3' DC I -48 " pdb=" C2' DC I -48 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 7.92e-01 ... (remaining 19058 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 25877 1.07 - 2.15: 874 2.15 - 3.22: 206 3.22 - 4.29: 17 4.29 - 5.36: 7 Bond angle restraints: 26981 Sorted by residual: angle pdb=" N ILE L 92 " pdb=" CA ILE L 92 " pdb=" C ILE L 92 " ideal model delta sigma weight residual 113.53 109.97 3.56 9.80e-01 1.04e+00 1.32e+01 angle pdb=" C4' DC I -20 " pdb=" O4' DC I -20 " pdb=" C1' DC I -20 " ideal model delta sigma weight residual 109.70 106.41 3.29 1.50e+00 4.44e-01 4.80e+00 angle pdb=" C ASN K 295 " pdb=" N SER K 296 " pdb=" CA SER K 296 " ideal model delta sigma weight residual 121.70 125.39 -3.69 1.80e+00 3.09e-01 4.19e+00 angle pdb=" N ILE K 226 " pdb=" CA ILE K 226 " pdb=" C ILE K 226 " ideal model delta sigma weight residual 111.67 109.77 1.90 9.50e-01 1.11e+00 4.01e+00 angle pdb=" C3' DA J -38 " pdb=" C2' DA J -38 " pdb=" C1' DA J -38 " ideal model delta sigma weight residual 101.60 104.60 -3.00 1.50e+00 4.44e-01 3.99e+00 ... (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 - 0.027: 2078 0.027 - 0.054: 706 0.054 - 0.081: 174 0.081 - 0.108: 74 0.108 - 0.135: 28 Chirality restraints: 3060 Sorted by residual: 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 chirality pdb=" CA ILE K 429 " pdb=" N ILE K 429 " pdb=" C ILE K 429 " pdb=" CB ILE K 429 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-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: 18.660 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 50.090 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 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 : 0.002 0.030 19063 Z= 0.125 Angle : 0.468 5.365 26981 Z= 0.303 Chirality : 0.032 0.135 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (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 TRP 0.002 0.000 TRP K 69 HIS 0.004 0.000 HIS B 75 PHE 0.004 0.000 PHE L 88 TYR 0.019 0.001 TYR B 72 ARG 0.001 0.000 ARG B 67 *********************** 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 fitting. rotamer outliers: 1 poor density : 473 time to evaluate : 1.545 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: 0.7637 (p) REVERT: B 84 MET cc_start: 0.6827 (mmm) cc_final: 0.6023 (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: 0.7241 (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: 0.4000 (mtp85) REVERT: N 32 TRP cc_start: 0.4096 (p-90) cc_final: 0.3820 (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: 0.7614 (mm) outliers start: 1 outliers final: 0 residues processed: 474 average time/residue: 0.3672 time to fit residues: 243.1745 Evaluate side-chains 291 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 137 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN C 24 GLN C 73 ASN D 44 GLN D 92 GLN F 93 GLN G 24 GLN H 46 HIS ** 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 367 HIS K 459 GLN ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN O 2 GLN O 41 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19063 Z= 0.302 Angle : 0.637 10.911 26981 Z= 0.362 Chirality : 0.040 0.298 3060 Planarity : 0.005 0.049 2427 Dihedral : 27.910 103.900 4833 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.13 % Allowed : 11.92 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1498 helix: 0.80 (0.18), residues: 827 sheet: -0.51 (0.47), residues: 115 loop : -1.56 (0.23), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 242 HIS 0.008 0.002 HIS F 75 PHE 0.026 0.002 PHE L 88 TYR 0.021 0.002 TYR K 461 ARG 0.008 0.001 ARG F 45 *********************** 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 318 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 276 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8182 (p) cc_final: 0.7878 (t) REVERT: A 59 GLU cc_start: 0.7528 (mp0) cc_final: 0.7152 (mp0) REVERT: A 90 MET cc_start: 0.7523 (mmm) cc_final: 0.7213 (mmm) REVERT: B 25 ASN cc_start: 0.7177 (m110) cc_final: 0.6786 (m110) REVERT: B 53 GLU cc_start: 0.7168 (mp0) cc_final: 0.6663 (mp0) REVERT: B 63 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7281 (mt-10) REVERT: B 84 MET cc_start: 0.6959 (mmm) cc_final: 0.6390 (mmt) REVERT: C 99 ARG cc_start: 0.6730 (mmt180) cc_final: 0.6258 (mtt90) REVERT: D 32 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7272 (mt-10) REVERT: D 48 ASP cc_start: 0.7946 (m-30) cc_final: 0.7442 (p0) REVERT: D 68 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7299 (mm-30) REVERT: D 105 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7895 (tptt) REVERT: D 113 LYS cc_start: 0.7529 (tttp) cc_final: 0.7274 (tttp) REVERT: D 117 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7952 (mmtt) REVERT: E 59 GLU cc_start: 0.7644 (pp20) cc_final: 0.7070 (pp20) REVERT: E 73 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7383 (tt0) REVERT: E 76 GLN cc_start: 0.7426 (tt0) cc_final: 0.7162 (pt0) REVERT: E 81 ASP cc_start: 0.8244 (t0) cc_final: 0.8026 (t0) REVERT: E 120 MET cc_start: 0.5189 (mmt) cc_final: 0.4782 (mmt) REVERT: E 123 ASP cc_start: 0.8266 (m-30) cc_final: 0.7898 (m-30) REVERT: F 43 VAL cc_start: 0.7914 (t) cc_final: 0.7358 (p) REVERT: F 59 LYS cc_start: 0.7003 (tppt) cc_final: 0.6522 (ttpt) REVERT: F 80 THR cc_start: 0.7664 (m) cc_final: 0.7296 (p) REVERT: G 90 ASP cc_start: 0.6817 (t0) cc_final: 0.5584 (t0) REVERT: G 99 ARG cc_start: 0.7428 (mpt180) cc_final: 0.6786 (mmp-170) REVERT: H 59 MET cc_start: 0.6643 (mmm) cc_final: 0.6325 (mmm) REVERT: H 110 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7382 (mt-10) REVERT: K 15 LYS cc_start: 0.7779 (tptp) cc_final: 0.7357 (mtpt) REVERT: K 107 ASP cc_start: 0.7095 (p0) cc_final: 0.6789 (p0) REVERT: K 111 ASP cc_start: 0.5708 (t0) cc_final: 0.4878 (t0) REVERT: K 114 LEU cc_start: 0.6971 (mm) cc_final: 0.6750 (tp) REVERT: K 130 MET cc_start: 0.7157 (ptt) cc_final: 0.6731 (ttt) REVERT: K 229 ASN cc_start: 0.8472 (m-40) cc_final: 0.8182 (t0) REVERT: K 388 MET cc_start: 0.7338 (mmm) cc_final: 0.6803 (mmm) REVERT: K 389 LYS cc_start: 0.7926 (pttt) cc_final: 0.7571 (ttmt) REVERT: L 7 GLN cc_start: 0.6120 (tm-30) cc_final: 0.5902 (tt0) REVERT: M 30 ARG cc_start: 0.5309 (mtt-85) cc_final: 0.5031 (mmm160) REVERT: M 35 GLN cc_start: 0.6879 (tp40) cc_final: 0.6670 (tp-100) REVERT: M 70 TYR cc_start: 0.5158 (m-80) cc_final: 0.4793 (m-80) REVERT: M 73 CYS cc_start: 0.1783 (t) cc_final: 0.0613 (t) REVERT: M 95 ARG cc_start: 0.5049 (mtt180) cc_final: 0.4568 (mtp-110) REVERT: N 80 LYS cc_start: 0.8152 (mttt) cc_final: 0.7934 (mmmt) REVERT: N 85 LEU cc_start: 0.6172 (mt) cc_final: 0.5912 (mp) REVERT: O 36 ILE cc_start: 0.6249 (mt) cc_final: 0.6035 (tp) REVERT: O 45 PHE cc_start: 0.7149 (t80) cc_final: 0.6933 (t80) outliers start: 42 outliers final: 25 residues processed: 305 average time/residue: 0.3335 time to fit residues: 147.6803 Evaluate side-chains 260 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 235 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 D residue 44 GLN 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 38 ASN Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 127 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 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 N residue 77 VAL Chi-restraints excluded: chain N residue 81 CYS Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 12 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 159 optimal weight: 0.9980 chunk 171 optimal weight: 0.0170 chunk 141 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN H 64 ASN K 53 ASN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 213 GLN ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 HIS M 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 19063 Z= 0.209 Angle : 0.545 11.781 26981 Z= 0.316 Chirality : 0.036 0.210 3060 Planarity : 0.003 0.034 2427 Dihedral : 27.795 103.528 4833 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.06 % Allowed : 13.71 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1498 helix: 1.54 (0.19), residues: 820 sheet: -0.18 (0.50), residues: 107 loop : -1.27 (0.23), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 242 HIS 0.006 0.001 HIS K 83 PHE 0.011 0.001 PHE K 216 TYR 0.019 0.001 TYR B 88 ARG 0.006 0.001 ARG K 177 *********************** 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 298 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 257 time to evaluate : 1.540 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 58 THR cc_start: 0.8251 (p) cc_final: 0.7942 (t) REVERT: A 59 GLU cc_start: 0.7565 (mp0) cc_final: 0.7119 (mp0) REVERT: B 24 ASP cc_start: 0.5720 (t0) cc_final: 0.5488 (t0) REVERT: B 25 ASN cc_start: 0.7192 (m110) cc_final: 0.6832 (m110) REVERT: B 53 GLU cc_start: 0.7203 (mp0) cc_final: 0.6935 (mp0) REVERT: B 63 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 84 MET cc_start: 0.7030 (mmm) cc_final: 0.6185 (mmm) REVERT: C 41 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6580 (tm-30) REVERT: C 99 ARG cc_start: 0.6925 (mmt180) cc_final: 0.6423 (mtt90) REVERT: D 48 ASP cc_start: 0.7911 (m-30) cc_final: 0.7314 (p0) REVERT: D 68 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7275 (mm-30) REVERT: D 98 LEU cc_start: 0.6890 (mm) cc_final: 0.6638 (mm) REVERT: D 105 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7664 (tptt) REVERT: E 59 GLU cc_start: 0.7438 (pp20) cc_final: 0.7038 (pp20) REVERT: E 73 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7458 (tt0) REVERT: E 76 GLN cc_start: 0.7361 (tt0) cc_final: 0.7141 (pt0) REVERT: E 123 ASP cc_start: 0.8210 (m-30) cc_final: 0.7898 (m-30) REVERT: F 43 VAL cc_start: 0.8034 (t) cc_final: 0.7509 (p) REVERT: F 59 LYS cc_start: 0.6973 (tppt) cc_final: 0.6521 (ttpt) REVERT: F 80 THR cc_start: 0.7575 (m) cc_final: 0.7089 (p) REVERT: G 90 ASP cc_start: 0.6349 (t0) cc_final: 0.5643 (t0) REVERT: G 99 ARG cc_start: 0.7439 (mpt180) cc_final: 0.6881 (mmp-170) REVERT: H 30 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7328 (ttm-80) REVERT: H 59 MET cc_start: 0.7057 (mmm) cc_final: 0.6806 (mmm) REVERT: H 110 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7351 (mt-10) REVERT: K 15 LYS cc_start: 0.7844 (tptp) cc_final: 0.7365 (mtpt) REVERT: K 107 ASP cc_start: 0.6920 (p0) cc_final: 0.6615 (p0) REVERT: K 111 ASP cc_start: 0.5816 (t0) cc_final: 0.4986 (t0) REVERT: K 130 MET cc_start: 0.7300 (ptt) cc_final: 0.6938 (ttt) REVERT: K 229 ASN cc_start: 0.8477 (m-40) cc_final: 0.8164 (t0) REVERT: K 388 MET cc_start: 0.7339 (mmm) cc_final: 0.6849 (mmm) REVERT: M 30 ARG cc_start: 0.5404 (mtt-85) cc_final: 0.4968 (mmm160) REVERT: M 81 SER cc_start: 0.6374 (OUTLIER) cc_final: 0.6014 (t) REVERT: M 95 ARG cc_start: 0.5126 (mtt180) cc_final: 0.4570 (mtp-110) REVERT: O 45 PHE cc_start: 0.7183 (t80) cc_final: 0.6976 (t80) outliers start: 41 outliers final: 28 residues processed: 284 average time/residue: 0.3161 time to fit residues: 131.3670 Evaluate side-chains 266 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 237 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain D residue 88 SER 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 38 ASN Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 10 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 257 LEU Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 470 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 81 SER Chi-restraints excluded: chain N residue 81 CYS Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 13 ASN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 HIS O 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19063 Z= 0.353 Angle : 0.645 11.009 26981 Z= 0.369 Chirality : 0.041 0.198 3060 Planarity : 0.004 0.048 2427 Dihedral : 28.396 95.637 4833 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.95 % Allowed : 14.83 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.22), residues: 1498 helix: 1.47 (0.19), residues: 811 sheet: -0.43 (0.45), residues: 131 loop : -1.22 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 242 HIS 0.006 0.001 HIS F 75 PHE 0.014 0.002 PHE K 216 TYR 0.020 0.002 TYR H 80 ARG 0.005 0.001 ARG E 49 *********************** 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 301 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 248 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8409 (p) cc_final: 0.8143 (t) REVERT: A 59 GLU cc_start: 0.7760 (mp0) cc_final: 0.7337 (mp0) REVERT: A 120 MET cc_start: 0.6668 (mmt) cc_final: 0.6191 (mtp) REVERT: B 53 GLU cc_start: 0.7338 (mp0) cc_final: 0.7128 (mp0) REVERT: B 84 MET cc_start: 0.6979 (mmm) cc_final: 0.6283 (mmm) REVERT: C 41 GLU cc_start: 0.6785 (tm-30) cc_final: 0.6544 (tm-30) REVERT: C 61 GLU cc_start: 0.6757 (tp30) cc_final: 0.6461 (tp30) REVERT: C 64 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7269 (tm-30) REVERT: C 72 ASP cc_start: 0.7003 (m-30) cc_final: 0.6731 (m-30) REVERT: C 90 ASP cc_start: 0.7658 (t0) cc_final: 0.6969 (t70) REVERT: C 92 GLU cc_start: 0.6816 (mp0) cc_final: 0.6518 (mp0) REVERT: C 99 ARG cc_start: 0.6815 (mmt180) cc_final: 0.6433 (mmt90) REVERT: D 48 ASP cc_start: 0.7713 (m-30) cc_final: 0.7159 (p0) REVERT: D 68 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7020 (mm-30) REVERT: D 102 GLU cc_start: 0.6913 (pm20) cc_final: 0.6655 (pm20) REVERT: D 105 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7881 (tptt) REVERT: E 59 GLU cc_start: 0.7827 (pp20) cc_final: 0.7286 (pp20) REVERT: E 123 ASP cc_start: 0.8028 (m-30) cc_final: 0.7642 (m-30) REVERT: F 59 LYS cc_start: 0.7047 (tppt) cc_final: 0.6697 (ttpt) REVERT: F 92 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6751 (ttm-80) REVERT: G 90 ASP cc_start: 0.6213 (t0) cc_final: 0.5527 (t0) REVERT: G 92 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7347 (mt-10) REVERT: G 99 ARG cc_start: 0.7368 (mpt180) cc_final: 0.6804 (mmp-170) REVERT: H 30 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7209 (ttm-80) REVERT: H 110 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7360 (mt-10) REVERT: K 15 LYS cc_start: 0.7581 (tptp) cc_final: 0.7223 (mtpt) REVERT: K 107 ASP cc_start: 0.6985 (p0) cc_final: 0.6744 (p0) REVERT: K 111 ASP cc_start: 0.5988 (t0) cc_final: 0.5431 (t0) REVERT: K 130 MET cc_start: 0.7360 (ptt) cc_final: 0.6912 (ttt) REVERT: K 229 ASN cc_start: 0.8364 (m-40) cc_final: 0.8106 (t0) REVERT: L 84 GLN cc_start: 0.7526 (mp10) cc_final: 0.7311 (mp10) REVERT: M 30 ARG cc_start: 0.5620 (mtt-85) cc_final: 0.5294 (mmm160) REVERT: M 95 ARG cc_start: 0.4852 (mtt180) cc_final: 0.4392 (mtp-110) outliers start: 53 outliers final: 37 residues processed: 281 average time/residue: 0.3138 time to fit residues: 129.4971 Evaluate side-chains 271 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 233 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 E residue 96 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG 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 G residue 56 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 23 THR 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 183 PHE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 299 THR Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 470 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 81 SER Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 81 CYS Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 12 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 HIS N 45 GLN O 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19063 Z= 0.196 Angle : 0.553 9.192 26981 Z= 0.319 Chirality : 0.036 0.170 3060 Planarity : 0.003 0.049 2427 Dihedral : 27.952 97.779 4833 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.58 % Allowed : 16.24 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.22), residues: 1498 helix: 1.84 (0.19), residues: 814 sheet: -0.41 (0.45), residues: 131 loop : -1.02 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 32 HIS 0.005 0.001 HIS K 83 PHE 0.040 0.001 PHE K 11 TYR 0.037 0.001 TYR H 80 ARG 0.009 0.000 ARG K 468 *********************** 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 305 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 257 time to evaluate : 1.794 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 58 THR cc_start: 0.8255 (p) cc_final: 0.7972 (t) REVERT: A 59 GLU cc_start: 0.7647 (mp0) cc_final: 0.7218 (mp0) REVERT: A 120 MET cc_start: 0.6536 (mmt) cc_final: 0.6028 (mtp) REVERT: B 53 GLU cc_start: 0.7485 (mp0) cc_final: 0.7283 (mp0) REVERT: B 84 MET cc_start: 0.7151 (mmm) cc_final: 0.6500 (mmm) REVERT: C 41 GLU cc_start: 0.6724 (tm-30) cc_final: 0.6461 (tm-30) REVERT: C 61 GLU cc_start: 0.6755 (tp30) cc_final: 0.6392 (tp30) REVERT: C 72 ASP cc_start: 0.7020 (m-30) cc_final: 0.6769 (m-30) REVERT: C 99 ARG cc_start: 0.6838 (mmt180) cc_final: 0.6460 (mmt90) REVERT: D 48 ASP cc_start: 0.7659 (m-30) cc_final: 0.7095 (p0) REVERT: D 68 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7247 (mm-30) REVERT: D 105 LYS cc_start: 0.7928 (ttmt) cc_final: 0.7668 (tptt) REVERT: E 59 GLU cc_start: 0.7565 (pp20) cc_final: 0.7078 (pp20) REVERT: E 123 ASP cc_start: 0.8144 (m-30) cc_final: 0.7785 (m-30) REVERT: F 43 VAL cc_start: 0.7673 (t) cc_final: 0.7030 (p) REVERT: F 59 LYS cc_start: 0.7004 (tppt) cc_final: 0.6586 (ttpt) REVERT: F 74 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7735 (mm-30) REVERT: G 64 GLU cc_start: 0.7020 (tp30) cc_final: 0.6463 (tp30) REVERT: G 68 ASN cc_start: 0.7092 (m-40) cc_final: 0.6663 (m-40) REVERT: G 90 ASP cc_start: 0.6056 (t0) cc_final: 0.5414 (t0) REVERT: G 99 ARG cc_start: 0.7525 (mpt180) cc_final: 0.6858 (mmp-170) REVERT: H 59 MET cc_start: 0.6654 (mmm) cc_final: 0.6231 (mmt) REVERT: H 90 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6515 (mt-10) REVERT: H 110 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7323 (mt-10) REVERT: K 15 LYS cc_start: 0.7795 (tptp) cc_final: 0.7321 (mtpt) REVERT: K 107 ASP cc_start: 0.6722 (p0) cc_final: 0.6489 (p0) REVERT: K 111 ASP cc_start: 0.5878 (t0) cc_final: 0.5442 (t0) REVERT: K 130 MET cc_start: 0.7251 (ptt) cc_final: 0.6787 (ttt) REVERT: K 229 ASN cc_start: 0.8277 (m-40) cc_final: 0.8027 (t0) REVERT: K 388 MET cc_start: 0.6888 (mmm) cc_final: 0.6648 (mmm) REVERT: M 30 ARG cc_start: 0.5575 (mtt-85) cc_final: 0.5154 (mmm160) REVERT: M 81 SER cc_start: 0.5830 (OUTLIER) cc_final: 0.5488 (t) REVERT: M 95 ARG cc_start: 0.4957 (mtt180) cc_final: 0.4344 (mtp-110) REVERT: N 80 LYS cc_start: 0.7683 (mmmt) cc_final: 0.7362 (mttt) outliers start: 48 outliers final: 36 residues processed: 279 average time/residue: 0.3206 time to fit residues: 131.1049 Evaluate side-chains 285 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 247 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG 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 G residue 56 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU 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 127 VAL Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 470 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 81 SER Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.5980 chunk 152 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 169 optimal weight: 0.2980 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 75 HIS ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 HIS O 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19063 Z= 0.189 Angle : 0.543 8.167 26981 Z= 0.314 Chirality : 0.036 0.181 3060 Planarity : 0.003 0.038 2427 Dihedral : 27.901 92.347 4833 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.83 % Allowed : 17.29 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1498 helix: 2.01 (0.19), residues: 813 sheet: -0.27 (0.47), residues: 122 loop : -1.10 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 242 HIS 0.005 0.001 HIS K 83 PHE 0.038 0.001 PHE K 11 TYR 0.042 0.001 TYR H 80 ARG 0.006 0.000 ARG K 177 *********************** 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 299 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 261 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8234 (p) cc_final: 0.7943 (t) REVERT: A 59 GLU cc_start: 0.7703 (mp0) cc_final: 0.7275 (mp0) REVERT: B 63 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6703 (mt-10) REVERT: B 84 MET cc_start: 0.7015 (mmm) cc_final: 0.6388 (mmm) REVERT: C 41 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6491 (tm-30) REVERT: C 61 GLU cc_start: 0.6516 (tp30) cc_final: 0.6306 (tp30) REVERT: C 72 ASP cc_start: 0.6946 (m-30) cc_final: 0.6669 (m-30) REVERT: C 99 ARG cc_start: 0.6794 (mmt180) cc_final: 0.6405 (mmt90) REVERT: D 48 ASP cc_start: 0.7688 (m-30) cc_final: 0.6963 (p0) REVERT: D 56 MET cc_start: 0.7957 (mmm) cc_final: 0.7743 (tpp) REVERT: D 68 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7239 (mm-30) REVERT: D 105 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7721 (tptt) REVERT: E 59 GLU cc_start: 0.7521 (pp20) cc_final: 0.7047 (pp20) REVERT: E 76 GLN cc_start: 0.7114 (tt0) cc_final: 0.6687 (pt0) REVERT: E 123 ASP cc_start: 0.8066 (m-30) cc_final: 0.7713 (m-30) REVERT: F 43 VAL cc_start: 0.7718 (t) cc_final: 0.7072 (p) REVERT: F 59 LYS cc_start: 0.6975 (tppt) cc_final: 0.6598 (ttpt) REVERT: F 84 MET cc_start: 0.6583 (mmm) cc_final: 0.6256 (mmt) REVERT: G 90 ASP cc_start: 0.5986 (t0) cc_final: 0.5392 (t0) REVERT: G 99 ARG cc_start: 0.7529 (mpt180) cc_final: 0.6863 (mmp-170) REVERT: H 59 MET cc_start: 0.6840 (mmm) cc_final: 0.6448 (mmt) REVERT: H 90 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6515 (mt-10) REVERT: H 110 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7334 (mt-10) REVERT: K 15 LYS cc_start: 0.7690 (tptp) cc_final: 0.7236 (mtpt) REVERT: K 107 ASP cc_start: 0.7023 (p0) cc_final: 0.6816 (p0) REVERT: K 111 ASP cc_start: 0.5761 (t0) cc_final: 0.5378 (t0) REVERT: K 130 MET cc_start: 0.7321 (ptt) cc_final: 0.6835 (ttt) REVERT: K 229 ASN cc_start: 0.8275 (m-40) cc_final: 0.8026 (t0) REVERT: K 388 MET cc_start: 0.7076 (mmm) cc_final: 0.6709 (mmm) REVERT: M 30 ARG cc_start: 0.5470 (mtt-85) cc_final: 0.5028 (mmm160) REVERT: M 67 SER cc_start: 0.4114 (p) cc_final: 0.3850 (m) REVERT: M 95 ARG cc_start: 0.4775 (mtt180) cc_final: 0.4271 (mtp-110) REVERT: N 65 ILE cc_start: 0.7072 (mm) cc_final: 0.6836 (mt) REVERT: N 80 LYS cc_start: 0.7724 (mmmt) cc_final: 0.7391 (mttt) outliers start: 38 outliers final: 33 residues processed: 282 average time/residue: 0.3319 time to fit residues: 138.7790 Evaluate side-chains 278 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 244 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 117 LYS 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 38 ASN Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 10 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 359 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 470 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain N residue 81 CYS Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 0.0030 chunk 94 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN F 64 ASN H 46 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19063 Z= 0.212 Angle : 0.568 12.421 26981 Z= 0.325 Chirality : 0.037 0.420 3060 Planarity : 0.003 0.042 2427 Dihedral : 27.921 93.144 4833 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.20 % Allowed : 17.06 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.22), residues: 1498 helix: 1.96 (0.19), residues: 815 sheet: -0.19 (0.47), residues: 122 loop : -1.11 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 38 HIS 0.005 0.001 HIS K 83 PHE 0.037 0.001 PHE K 11 TYR 0.020 0.001 TYR L 15 ARG 0.007 0.000 ARG K 133 *********************** 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 297 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 254 time to evaluate : 1.605 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 58 THR cc_start: 0.8244 (p) cc_final: 0.7955 (t) REVERT: A 59 GLU cc_start: 0.7624 (mp0) cc_final: 0.7198 (mp0) REVERT: B 24 ASP cc_start: 0.4817 (t0) cc_final: 0.4513 (t0) REVERT: B 63 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6869 (mt-10) REVERT: B 84 MET cc_start: 0.6962 (mmm) cc_final: 0.6339 (mmm) REVERT: C 72 ASP cc_start: 0.6962 (m-30) cc_final: 0.6684 (m-30) REVERT: C 99 ARG cc_start: 0.6895 (mmt180) cc_final: 0.6476 (mmt90) REVERT: D 48 ASP cc_start: 0.7611 (m-30) cc_final: 0.6899 (p0) REVERT: D 68 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7252 (mm-30) REVERT: D 105 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7729 (tptt) REVERT: E 59 GLU cc_start: 0.7605 (pp20) cc_final: 0.7102 (pp20) REVERT: E 76 GLN cc_start: 0.6941 (tt0) cc_final: 0.6487 (pt0) REVERT: E 106 ASP cc_start: 0.6751 (m-30) cc_final: 0.6550 (m-30) REVERT: E 123 ASP cc_start: 0.8068 (m-30) cc_final: 0.7708 (m-30) REVERT: F 43 VAL cc_start: 0.7633 (t) cc_final: 0.6956 (p) REVERT: F 59 LYS cc_start: 0.6979 (tppt) cc_final: 0.6581 (ttpt) REVERT: G 90 ASP cc_start: 0.6126 (t0) cc_final: 0.5659 (t0) REVERT: G 99 ARG cc_start: 0.7544 (mpt180) cc_final: 0.6918 (mmp-170) REVERT: H 59 MET cc_start: 0.6668 (mmm) cc_final: 0.6216 (mmm) REVERT: H 90 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6514 (mt-10) REVERT: K 107 ASP cc_start: 0.6957 (p0) cc_final: 0.6741 (p0) REVERT: K 111 ASP cc_start: 0.5797 (t0) cc_final: 0.5231 (t0) REVERT: K 130 MET cc_start: 0.7351 (ptt) cc_final: 0.6977 (ttt) REVERT: K 229 ASN cc_start: 0.8214 (m-40) cc_final: 0.7994 (t0) REVERT: K 388 MET cc_start: 0.7024 (mmm) cc_final: 0.6565 (mmm) REVERT: M 30 ARG cc_start: 0.5484 (mtt-85) cc_final: 0.5159 (mmm160) REVERT: M 95 ARG cc_start: 0.4722 (mtt180) cc_final: 0.4220 (mtp-110) REVERT: N 65 ILE cc_start: 0.6963 (mm) cc_final: 0.6750 (mt) REVERT: N 80 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7402 (mttt) outliers start: 43 outliers final: 38 residues processed: 277 average time/residue: 0.3078 time to fit residues: 126.4849 Evaluate side-chains 281 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 117 LYS 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 38 ASN Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 10 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 299 THR Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 470 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 132 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 HIS O 49 GLN O 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19063 Z= 0.188 Angle : 0.561 16.255 26981 Z= 0.320 Chirality : 0.037 0.386 3060 Planarity : 0.003 0.040 2427 Dihedral : 27.837 94.631 4833 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.65 % Allowed : 17.21 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.22), residues: 1498 helix: 1.98 (0.19), residues: 815 sheet: -0.24 (0.45), residues: 132 loop : -1.06 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 118 HIS 0.004 0.001 HIS K 83 PHE 0.035 0.001 PHE K 11 TYR 0.040 0.001 TYR F 88 ARG 0.007 0.000 ARG K 133 *********************** 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 301 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 252 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8201 (p) cc_final: 0.7919 (t) REVERT: A 59 GLU cc_start: 0.7586 (mp0) cc_final: 0.7163 (mp0) REVERT: B 24 ASP cc_start: 0.5516 (t0) cc_final: 0.5139 (t0) REVERT: B 63 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6838 (mt-10) REVERT: B 84 MET cc_start: 0.6913 (mmm) cc_final: 0.6282 (mmm) REVERT: C 72 ASP cc_start: 0.6955 (m-30) cc_final: 0.6681 (m-30) REVERT: C 99 ARG cc_start: 0.6909 (mmt180) cc_final: 0.6481 (mmt90) REVERT: D 48 ASP cc_start: 0.7591 (m-30) cc_final: 0.6874 (p0) REVERT: D 68 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7231 (mm-30) REVERT: D 105 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7699 (tptt) REVERT: E 76 GLN cc_start: 0.6923 (tt0) cc_final: 0.6467 (pt0) REVERT: E 123 ASP cc_start: 0.8078 (m-30) cc_final: 0.7720 (m-30) REVERT: F 43 VAL cc_start: 0.7675 (t) cc_final: 0.7013 (p) REVERT: F 59 LYS cc_start: 0.6970 (tppt) cc_final: 0.6574 (ttpt) REVERT: F 92 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6649 (ttm-80) REVERT: G 90 ASP cc_start: 0.6100 (t0) cc_final: 0.5640 (t0) REVERT: G 99 ARG cc_start: 0.7544 (mpt180) cc_final: 0.6913 (mmp-170) REVERT: H 59 MET cc_start: 0.6699 (mmm) cc_final: 0.6282 (mmt) REVERT: H 90 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6494 (mt-10) REVERT: K 107 ASP cc_start: 0.6800 (p0) cc_final: 0.6569 (p0) REVERT: K 111 ASP cc_start: 0.5816 (t0) cc_final: 0.5244 (t0) REVERT: K 130 MET cc_start: 0.7415 (ptt) cc_final: 0.7057 (ttt) REVERT: K 229 ASN cc_start: 0.8197 (m-40) cc_final: 0.7963 (t0) REVERT: K 388 MET cc_start: 0.7022 (mmm) cc_final: 0.6541 (mmm) REVERT: M 30 ARG cc_start: 0.5524 (mtt-85) cc_final: 0.5170 (mmm160) REVERT: M 95 ARG cc_start: 0.4859 (mtt180) cc_final: 0.4425 (mtm110) REVERT: N 65 ILE cc_start: 0.6956 (mm) cc_final: 0.6750 (mt) REVERT: N 80 LYS cc_start: 0.7709 (mmmt) cc_final: 0.7372 (mttt) outliers start: 49 outliers final: 44 residues processed: 279 average time/residue: 0.3170 time to fit residues: 130.9071 Evaluate side-chains 290 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 244 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 92 GLU 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 88 SER Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG 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 G residue 56 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 299 THR Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 470 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 chunk 156 optimal weight: 0.4980 chunk 103 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19063 Z= 0.211 Angle : 0.574 16.474 26981 Z= 0.327 Chirality : 0.037 0.377 3060 Planarity : 0.003 0.044 2427 Dihedral : 27.892 95.004 4833 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.58 % Allowed : 17.29 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.22), residues: 1498 helix: 1.89 (0.19), residues: 819 sheet: -0.19 (0.46), residues: 132 loop : -1.04 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 118 HIS 0.004 0.001 HIS K 83 PHE 0.034 0.001 PHE K 11 TYR 0.014 0.001 TYR B 88 ARG 0.010 0.000 ARG K 468 *********************** 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 297 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 249 time to evaluate : 2.156 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 58 THR cc_start: 0.8165 (p) cc_final: 0.7876 (t) REVERT: A 59 GLU cc_start: 0.7586 (mp0) cc_final: 0.7156 (mp0) REVERT: B 24 ASP cc_start: 0.5891 (t0) cc_final: 0.5575 (t0) REVERT: B 63 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6836 (mt-10) REVERT: B 84 MET cc_start: 0.6943 (mmm) cc_final: 0.6337 (mmm) REVERT: C 41 GLU cc_start: 0.7674 (tt0) cc_final: 0.7430 (tm-30) REVERT: C 72 ASP cc_start: 0.6964 (m-30) cc_final: 0.6689 (m-30) REVERT: C 99 ARG cc_start: 0.6909 (mmt180) cc_final: 0.6457 (mmt90) REVERT: D 48 ASP cc_start: 0.7593 (m-30) cc_final: 0.6864 (p0) REVERT: D 68 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7256 (mm-30) REVERT: D 105 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7647 (tptt) REVERT: E 76 GLN cc_start: 0.7051 (tt0) cc_final: 0.6675 (pt0) REVERT: E 123 ASP cc_start: 0.8072 (m-30) cc_final: 0.7708 (m-30) REVERT: F 43 VAL cc_start: 0.7800 (t) cc_final: 0.7198 (p) REVERT: F 59 LYS cc_start: 0.6985 (tppt) cc_final: 0.6609 (ttpt) REVERT: F 92 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6642 (ttm-80) REVERT: G 90 ASP cc_start: 0.6098 (t0) cc_final: 0.5640 (t0) REVERT: G 99 ARG cc_start: 0.7628 (mpt180) cc_final: 0.6985 (mmp-170) REVERT: H 59 MET cc_start: 0.6664 (mmm) cc_final: 0.6206 (mmm) REVERT: H 90 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6501 (mt-10) REVERT: K 107 ASP cc_start: 0.6816 (p0) cc_final: 0.6590 (p0) REVERT: K 111 ASP cc_start: 0.5878 (t0) cc_final: 0.5272 (t0) REVERT: K 130 MET cc_start: 0.7406 (ptt) cc_final: 0.7037 (ttt) REVERT: K 229 ASN cc_start: 0.8204 (m-40) cc_final: 0.7928 (t0) REVERT: K 388 MET cc_start: 0.7015 (mmm) cc_final: 0.6496 (mmm) REVERT: M 30 ARG cc_start: 0.5511 (mtt-85) cc_final: 0.5250 (mmm160) REVERT: M 95 ARG cc_start: 0.4858 (mtt180) cc_final: 0.4425 (mtm110) REVERT: N 45 GLN cc_start: 0.6507 (tp40) cc_final: 0.6003 (mm-40) outliers start: 48 outliers final: 45 residues processed: 276 average time/residue: 0.3148 time to fit residues: 130.0100 Evaluate side-chains 294 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 247 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG 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 G residue 56 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 299 THR Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 470 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 160 optimal weight: 0.0170 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 35 GLN M 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19063 Z= 0.269 Angle : 0.610 16.808 26981 Z= 0.346 Chirality : 0.039 0.372 3060 Planarity : 0.004 0.050 2427 Dihedral : 28.056 94.219 4833 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.43 % Allowed : 17.81 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1498 helix: 1.78 (0.19), residues: 817 sheet: -0.28 (0.45), residues: 132 loop : -1.11 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 118 HIS 0.005 0.001 HIS K 83 PHE 0.036 0.002 PHE K 11 TYR 0.042 0.002 TYR F 88 ARG 0.010 0.001 ARG K 468 ********************** 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 291 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 245 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8307 (p) cc_final: 0.8023 (t) REVERT: A 59 GLU cc_start: 0.7642 (mp0) cc_final: 0.7200 (mp0) REVERT: A 120 MET cc_start: 0.6601 (mmt) cc_final: 0.6098 (mtp) REVERT: B 63 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6864 (mt-10) REVERT: B 84 MET cc_start: 0.6935 (mmm) cc_final: 0.6449 (mmm) REVERT: C 72 ASP cc_start: 0.7158 (m-30) cc_final: 0.6770 (m-30) REVERT: C 91 GLU cc_start: 0.7065 (pm20) cc_final: 0.6850 (pm20) REVERT: C 99 ARG cc_start: 0.6862 (mmt180) cc_final: 0.6444 (mmt90) REVERT: D 48 ASP cc_start: 0.7619 (m-30) cc_final: 0.6897 (p0) REVERT: D 68 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7267 (mm-30) REVERT: D 105 LYS cc_start: 0.8042 (ttmt) cc_final: 0.7733 (tptt) REVERT: D 113 LYS cc_start: 0.7601 (tttp) cc_final: 0.7364 (ttmm) REVERT: E 76 GLN cc_start: 0.7067 (tt0) cc_final: 0.6723 (pt0) REVERT: E 123 ASP cc_start: 0.8053 (m-30) cc_final: 0.7656 (m-30) REVERT: F 59 LYS cc_start: 0.7000 (tppt) cc_final: 0.6603 (ttpt) REVERT: F 92 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6531 (ttm-80) REVERT: G 90 ASP cc_start: 0.6019 (t0) cc_final: 0.5414 (t0) REVERT: G 99 ARG cc_start: 0.7502 (mpt180) cc_final: 0.6821 (mmp-170) REVERT: H 59 MET cc_start: 0.6651 (mmm) cc_final: 0.6209 (mmm) REVERT: H 90 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6473 (mt-10) REVERT: K 107 ASP cc_start: 0.6968 (p0) cc_final: 0.6765 (p0) REVERT: K 111 ASP cc_start: 0.6011 (t0) cc_final: 0.5405 (t0) REVERT: K 130 MET cc_start: 0.7390 (ptt) cc_final: 0.7018 (ttt) REVERT: K 229 ASN cc_start: 0.8160 (m-40) cc_final: 0.7896 (t0) REVERT: K 388 MET cc_start: 0.7002 (mmm) cc_final: 0.6504 (mmm) REVERT: M 30 ARG cc_start: 0.5723 (mtt-85) cc_final: 0.5468 (mmm160) REVERT: M 95 ARG cc_start: 0.4845 (mtt180) cc_final: 0.4386 (mtm110) REVERT: N 80 LYS cc_start: 0.7602 (mmmt) cc_final: 0.7238 (mttt) outliers start: 46 outliers final: 40 residues processed: 272 average time/residue: 0.3078 time to fit residues: 124.2545 Evaluate side-chains 279 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 237 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 92 ARG 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 G residue 56 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 299 THR Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 408 ASP Chi-restraints excluded: chain K residue 470 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 12 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 139 optimal weight: 0.0970 chunk 58 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 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 = 0.3664 r_free = 0.3664 target = 0.097236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.071371 restraints weight = 50943.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.073163 restraints weight = 27049.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.074351 restraints weight = 18257.786| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19063 Z= 0.187 Angle : 0.575 17.067 26981 Z= 0.328 Chirality : 0.037 0.375 3060 Planarity : 0.004 0.043 2427 Dihedral : 27.826 96.830 4833 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.06 % Allowed : 18.70 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1498 helix: 1.93 (0.19), residues: 816 sheet: -0.32 (0.45), residues: 134 loop : -1.09 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 38 HIS 0.004 0.001 HIS K 83 PHE 0.034 0.001 PHE K 11 TYR 0.023 0.001 TYR F 88 ARG 0.009 0.000 ARG K 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3693.86 seconds wall clock time: 66 minutes 55.73 seconds (4015.73 seconds total)