Starting phenix.real_space_refine on Mon Sep 30 00:40:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk2_27481/09_2024/8dk2_27481.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk2_27481/09_2024/8dk2_27481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk2_27481/09_2024/8dk2_27481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk2_27481/09_2024/8dk2_27481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk2_27481/09_2024/8dk2_27481.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk2_27481/09_2024/8dk2_27481.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.020 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 P 58 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 14634 2.51 5 N 4387 2.21 5 O 4595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23727 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3527 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2738 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 329} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5720 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 17, 'TRANS': 705} Chain breaks: 2 Chain: "D" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5680 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 17, 'TRANS': 700} Chain breaks: 2 Chain: "F" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 507 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "G" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "H" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1413 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 2 Chain: "I" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "P" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "Q" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.29, per 1000 atoms: 0.60 Number of scatterers: 23727 At special positions: 0 Unit cell: (168.67, 145.203, 288.94, 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) S 51 16.00 P 58 15.00 Mg 2 11.99 O 4595 8.00 N 4387 7.00 C 14634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.17 Conformation dependent library (CDL) restraints added in 3.2 seconds 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5340 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 16 sheets defined 65.9% alpha, 8.5% beta 26 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 8.35 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.513A pdb=" N SER A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 27 Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 52 through 63 removed outlier: 4.174A pdb=" N ALA A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.844A pdb=" N GLU A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 143 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.829A pdb=" N SER A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 220 removed outlier: 3.666A pdb=" N VAL A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.907A pdb=" N VAL A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 272 removed outlier: 4.064A pdb=" N LEU A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.603A pdb=" N ALA A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 removed outlier: 3.727A pdb=" N TRP A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 320 removed outlier: 3.517A pdb=" N ARG A 294 " --> pdb=" O TRP A 290 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 304 " --> pdb=" O GLN A 300 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 409 through 425 removed outlier: 4.176A pdb=" N LEU A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 445 through 457 Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 19 through 26 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 52 through 63 removed outlier: 4.170A pdb=" N ALA B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 3.630A pdb=" N ARG B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 117 removed outlier: 3.553A pdb=" N GLU B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 117 " --> pdb=" O PHE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 143 Processing helix chain 'B' and resid 146 through 170 removed outlier: 3.603A pdb=" N ARG B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 194 removed outlier: 3.645A pdb=" N SER B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 220 removed outlier: 4.093A pdb=" N VAL B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.806A pdb=" N VAL B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 256 through 272 removed outlier: 3.815A pdb=" N LEU B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 290 through 320 removed outlier: 3.534A pdb=" N VAL B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 304 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 339 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.510A pdb=" N LEU C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 86 removed outlier: 3.547A pdb=" N TYR C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.517A pdb=" N LEU C 139 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 164 through 175 removed outlier: 4.014A pdb=" N MET C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 174 " --> pdb=" O GLN C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.516A pdb=" N PHE C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.872A pdb=" N ILE C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.973A pdb=" N GLU C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 342 removed outlier: 4.530A pdb=" N LEU C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Proline residue: C 264 - end of helix Proline residue: C 290 - end of helix removed outlier: 3.637A pdb=" N ARG C 342 " --> pdb=" O GLN C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 741 removed outlier: 3.774A pdb=" N LYS C 696 " --> pdb=" O LEU C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.604A pdb=" N ALA C 755 " --> pdb=" O GLU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 808 Processing helix chain 'C' and resid 820 through 848 removed outlier: 4.313A pdb=" N ARG C 824 " --> pdb=" O VAL C 820 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU C 837 " --> pdb=" O THR C 833 " (cutoff:3.500A) Proline residue: C 838 - end of helix removed outlier: 4.248A pdb=" N GLU C 846 " --> pdb=" O LYS C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 881 removed outlier: 3.768A pdb=" N VAL C 856 " --> pdb=" O SER C 852 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 863 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR C 880 " --> pdb=" O ASP C 876 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 918 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 947 through 955 Processing helix chain 'C' and resid 956 through 958 No H-bonds generated for 'chain 'C' and resid 956 through 958' Processing helix chain 'C' and resid 985 through 1005 removed outlier: 3.704A pdb=" N LYS C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 990 " --> pdb=" O GLY C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1010 Processing helix chain 'C' and resid 1028 through 1042 Processing helix chain 'C' and resid 1055 through 1062 Processing helix chain 'C' and resid 1082 through 1087 removed outlier: 3.694A pdb=" N GLU C1087 " --> pdb=" O GLU C1083 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 79 through 86 Processing helix chain 'D' and resid 152 through 163 Processing helix chain 'D' and resid 164 through 170 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 200 through 209 removed outlier: 3.570A pdb=" N ALA D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.550A pdb=" N ILE D 220 " --> pdb=" O SER D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 242 through 341 removed outlier: 4.358A pdb=" N THR D 246 " --> pdb=" O PHE D 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 247 " --> pdb=" O ASP D 243 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Proline residue: D 264 - end of helix removed outlier: 4.121A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Proline residue: D 290 - end of helix Processing helix chain 'D' and resid 692 through 741 Processing helix chain 'D' and resid 748 through 757 removed outlier: 3.586A pdb=" N LEU D 752 " --> pdb=" O THR D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 763 No H-bonds generated for 'chain 'D' and resid 761 through 763' Processing helix chain 'D' and resid 764 through 808 Processing helix chain 'D' and resid 820 through 835 removed outlier: 4.220A pdb=" N ARG D 824 " --> pdb=" O VAL D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 848 removed outlier: 4.152A pdb=" N GLU D 839 " --> pdb=" O GLU D 835 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE D 844 " --> pdb=" O LYS D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 882 removed outlier: 4.303A pdb=" N VAL D 856 " --> pdb=" O SER D 852 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER D 879 " --> pdb=" O ASP D 875 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR D 880 " --> pdb=" O ASP D 876 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN D 882 " --> pdb=" O ASN D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 918 removed outlier: 3.550A pdb=" N ARG D 918 " --> pdb=" O LEU D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 944 removed outlier: 3.718A pdb=" N HIS D 944 " --> pdb=" O ASP D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 955 Processing helix chain 'D' and resid 956 through 958 No H-bonds generated for 'chain 'D' and resid 956 through 958' Processing helix chain 'D' and resid 985 through 1005 Processing helix chain 'D' and resid 1028 through 1042 removed outlier: 3.672A pdb=" N PHE D1042 " --> pdb=" O ALA D1038 " (cutoff:3.500A) Processing helix chain 'D' and resid 1054 through 1061 removed outlier: 3.784A pdb=" N HIS D1060 " --> pdb=" O ARG D1056 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 63 Processing helix chain 'F' and resid 70 through 79 Processing helix chain 'F' and resid 80 through 89 Processing helix chain 'G' and resid 49 through 63 Processing helix chain 'G' and resid 70 through 79 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 130 through 150 removed outlier: 3.705A pdb=" N GLU G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 174 Proline residue: G 167 - end of helix removed outlier: 3.850A pdb=" N TYR G 172 " --> pdb=" O GLN G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 195 Processing helix chain 'G' and resid 212 through 218 removed outlier: 4.140A pdb=" N HIS G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 235 Processing helix chain 'H' and resid 49 through 63 Processing helix chain 'H' and resid 70 through 79 Processing helix chain 'H' and resid 80 through 89 Processing helix chain 'H' and resid 130 through 150 removed outlier: 4.204A pdb=" N LEU H 136 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 174 removed outlier: 3.646A pdb=" N ILE H 166 " --> pdb=" O VAL H 162 " (cutoff:3.500A) Proline residue: H 167 - end of helix removed outlier: 4.278A pdb=" N TYR H 172 " --> pdb=" O GLN H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 196 removed outlier: 3.590A pdb=" N HIS H 196 " --> pdb=" O GLN H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'H' and resid 219 through 236 Processing helix chain 'I' and resid 49 through 63 Processing helix chain 'I' and resid 70 through 79 Processing helix chain 'I' and resid 80 through 89 Processing helix chain 'I' and resid 130 through 150 removed outlier: 3.825A pdb=" N GLU I 150 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 174 Proline residue: I 167 - end of helix removed outlier: 3.831A pdb=" N TYR I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 195 removed outlier: 3.516A pdb=" N GLU I 182 " --> pdb=" O SER I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 218 removed outlier: 4.114A pdb=" N HIS I 216 " --> pdb=" O PRO I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 460 through 472 removed outlier: 7.897A pdb=" N GLU A 463 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 10.549A pdb=" N LEU A 482 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ARG A 465 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N PHE A 480 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N PHE A 467 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N TRP A 478 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLU A 469 " --> pdb=" O GLN A 476 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N GLN A 476 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA4, first strand: chain 'C' and resid 29 through 33 removed outlier: 7.232A pdb=" N THR C 113 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE C 18 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA C 111 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU C 20 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ALA C 109 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 112 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 116 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY C 124 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1018 through 1021 removed outlier: 3.528A pdb=" N LEU C1020 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C1049 " --> pdb=" O LEU C1020 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR C 39 " --> pdb=" O PHE C1048 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 890 through 898 removed outlier: 3.754A pdb=" N GLU C 976 " --> pdb=" O VAL C 966 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 968 " --> pdb=" O LEU C 974 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU C 974 " --> pdb=" O ASP C 968 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 33 removed outlier: 7.001A pdb=" N THR D 113 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ILE D 18 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALA D 111 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU D 20 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA D 109 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 1017 through 1019 removed outlier: 7.025A pdb=" N THR D 39 " --> pdb=" O PHE D1048 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N THR D1050 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL D 41 " --> pdb=" O THR D1050 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 40 " --> pdb=" O SER D1064 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D1068 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA D1065 " --> pdb=" O LEU D1080 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 890 through 898 removed outlier: 3.980A pdb=" N GLU D 976 " --> pdb=" O VAL D 966 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP D 968 " --> pdb=" O LEU D 974 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU D 974 " --> pdb=" O ASP D 968 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AB2, first strand: chain 'G' and resid 64 through 66 Processing sheet with id=AB3, first strand: chain 'G' and resid 158 through 161 removed outlier: 4.746A pdb=" N ALA G 158 " --> pdb=" O ILE G 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 64 through 66 Processing sheet with id=AB5, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.164A pdb=" N ALA H 158 " --> pdb=" O ILE H 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 64 through 66 Processing sheet with id=AB7, first strand: chain 'I' and resid 159 through 161 1426 hydrogen bonds defined for protein. 4218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 8.60 Time building geometry restraints manager: 8.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 8289 1.36 - 1.51: 5987 1.51 - 1.65: 9836 1.65 - 1.80: 49 1.80 - 1.95: 37 Bond restraints: 24198 Sorted by residual: bond pdb=" CA LEU D 289 " pdb=" C LEU D 289 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.58e+00 bond pdb=" CA GLN D 263 " pdb=" C GLN D 263 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.26e-02 6.30e+03 1.32e+00 bond pdb=" CA GLN C 263 " pdb=" C GLN C 263 " ideal model delta sigma weight residual 1.521 1.535 -0.013 1.17e-02 7.31e+03 1.31e+00 bond pdb=" N LEU D 289 " pdb=" CA LEU D 289 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.41e-02 5.03e+03 1.30e+00 bond pdb=" C LEU D 289 " pdb=" O LEU D 289 " ideal model delta sigma weight residual 1.238 1.251 -0.014 1.28e-02 6.10e+03 1.13e+00 ... (remaining 24193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 32443 1.57 - 3.14: 415 3.14 - 4.71: 53 4.71 - 6.28: 10 6.28 - 7.85: 3 Bond angle restraints: 32924 Sorted by residual: angle pdb=" C ALA C 231 " pdb=" N PHE C 232 " pdb=" CA PHE C 232 " ideal model delta sigma weight residual 121.54 128.74 -7.20 1.91e+00 2.74e-01 1.42e+01 angle pdb=" N LEU D 289 " pdb=" CA LEU D 289 " pdb=" C LEU D 289 " ideal model delta sigma weight residual 109.81 117.24 -7.43 2.21e+00 2.05e-01 1.13e+01 angle pdb=" N VAL C1073 " pdb=" CA VAL C1073 " pdb=" C VAL C1073 " ideal model delta sigma weight residual 113.20 110.46 2.74 9.60e-01 1.09e+00 8.12e+00 angle pdb=" C SER C 230 " pdb=" N ALA C 231 " pdb=" CA ALA C 231 " ideal model delta sigma weight residual 121.54 126.10 -4.56 1.91e+00 2.74e-01 5.69e+00 angle pdb=" CA LEU D 860 " pdb=" CB LEU D 860 " pdb=" CG LEU D 860 " ideal model delta sigma weight residual 116.30 124.15 -7.85 3.50e+00 8.16e-02 5.02e+00 ... (remaining 32919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 14034 26.56 - 53.12: 625 53.12 - 79.68: 55 79.68 - 106.23: 4 106.23 - 132.79: 1 Dihedral angle restraints: 14719 sinusoidal: 6503 harmonic: 8216 Sorted by residual: dihedral pdb=" O1A AGS C1201 " pdb=" O3A AGS C1201 " pdb=" PA AGS C1201 " pdb=" PB AGS C1201 " ideal model delta sinusoidal sigma weight residual -67.73 65.06 -132.79 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" CA THR C1050 " pdb=" C THR C1050 " pdb=" N PRO C1051 " pdb=" CA PRO C1051 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLN A 18 " pdb=" C GLN A 18 " pdb=" N HIS A 19 " pdb=" CA HIS A 19 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 14716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2397 0.025 - 0.050: 776 0.050 - 0.075: 337 0.075 - 0.101: 132 0.101 - 0.126: 76 Chirality restraints: 3718 Sorted by residual: chirality pdb=" CA ILE D1049 " pdb=" N ILE D1049 " pdb=" C ILE D1049 " pdb=" CB ILE D1049 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE C1049 " pdb=" N ILE C1049 " pdb=" C ILE C1049 " pdb=" CB ILE C1049 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA VAL A 485 " pdb=" N VAL A 485 " pdb=" C VAL A 485 " pdb=" CB VAL A 485 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 3715 not shown) Planarity restraints: 4130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 780 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C GLN D 780 " 0.031 2.00e-02 2.50e+03 pdb=" O GLN D 780 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY D 781 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 783 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C LEU D 783 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU D 783 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS D 784 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 782 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C GLN D 782 " -0.030 2.00e-02 2.50e+03 pdb=" O GLN D 782 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU D 783 " 0.010 2.00e-02 2.50e+03 ... (remaining 4127 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 193 2.57 - 3.15: 19087 3.15 - 3.74: 37455 3.74 - 4.32: 47077 4.32 - 4.90: 77901 Nonbonded interactions: 181713 Sorted by model distance: nonbonded pdb=" NH2 ARG D 78 " pdb="MG MG D1202 " model vdw 1.988 2.250 nonbonded pdb=" N ALA C 69 " pdb="MG MG C1202 " model vdw 2.030 2.250 nonbonded pdb=" NE ARG D 78 " pdb="MG MG D1202 " model vdw 2.047 2.250 nonbonded pdb=" N SER C 70 " pdb="MG MG C1202 " model vdw 2.098 2.250 nonbonded pdb=" O ASN C 67 " pdb="MG MG C1202 " model vdw 2.102 2.170 ... (remaining 181708 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 'C' and (resid 10 through 1083 or resid 1201 through 1202)) selection = chain 'D' } ncs_group { reference = (chain 'G' and (resid 48 through 110 or resid 120 through 151 or resid 156 throu \ gh 236)) selection = chain 'H' selection = (chain 'I' and (resid 48 through 110 or resid 120 through 151 or resid 156 throu \ gh 236)) } 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: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 61.220 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.120 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 0.039 24198 Z= 0.158 Angle : 0.466 7.846 32924 Z= 0.256 Chirality : 0.035 0.126 3718 Planarity : 0.004 0.044 4130 Dihedral : 13.702 132.792 9379 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.88 % Allowed : 5.42 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.17), residues: 2798 helix: 2.62 (0.13), residues: 1708 sheet: -0.02 (0.33), residues: 279 loop : -0.97 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 128 HIS 0.003 0.001 HIS D 901 PHE 0.010 0.001 PHE D 187 TYR 0.011 0.001 TYR C 272 ARG 0.002 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 162 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8359 (mtp) cc_final: 0.8067 (ttm) REVERT: A 122 MET cc_start: 0.9243 (mtp) cc_final: 0.8740 (mpp) REVERT: A 260 LEU cc_start: 0.9278 (mt) cc_final: 0.8719 (mt) REVERT: A 452 MET cc_start: 0.9133 (mtp) cc_final: 0.8694 (mtt) REVERT: A 484 TYR cc_start: 0.8502 (t80) cc_final: 0.8031 (t80) REVERT: B 25 LEU cc_start: 0.9134 (mt) cc_final: 0.8865 (pp) REVERT: B 122 MET cc_start: 0.9512 (mtp) cc_final: 0.9122 (pmm) REVERT: B 144 ASN cc_start: 0.8270 (t0) cc_final: 0.7827 (t0) REVERT: B 176 LEU cc_start: 0.8383 (mt) cc_final: 0.8041 (tp) REVERT: B 325 HIS cc_start: 0.9065 (m170) cc_final: 0.8814 (t-170) REVERT: C 801 MET cc_start: 0.7573 (tmm) cc_final: 0.7095 (tmm) REVERT: C 901 HIS cc_start: 0.8159 (p-80) cc_final: 0.7805 (p-80) REVERT: C 953 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9361 (tt) REVERT: D 19 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: D 227 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8176 (t70) REVERT: D 1060 HIS cc_start: 0.8200 (OUTLIER) cc_final: 0.7862 (m170) REVERT: F 74 TYR cc_start: 0.6652 (t80) cc_final: 0.6069 (t80) REVERT: H 95 MET cc_start: 0.1587 (ttp) cc_final: -0.0813 (mmt) outliers start: 69 outliers final: 23 residues processed: 229 average time/residue: 0.3859 time to fit residues: 136.5050 Evaluate side-chains 111 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 163 HIS ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN B 133 GLN B 163 HIS B 240 ASN C 97 GLN C 99 HIS C 103 GLN C 258 GLN C 276 GLN C 329 GLN C 336 HIS C 775 HIS C 858 GLN C1060 HIS D 312 HIS D 712 GLN D 726 GLN F 57 GLN G 57 GLN G 80 ASN G 110 GLN G 116 GLN G 127 GLN G 149 GLN G 157 GLN G 196 HIS G 216 HIS H 57 GLN H 69 HIS H 205 HIS I 57 GLN I 80 ASN I 110 GLN I 127 GLN I 142 GLN I 149 GLN I 157 GLN I 168 GLN I 224 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24198 Z= 0.258 Angle : 0.593 8.413 32924 Z= 0.312 Chirality : 0.039 0.151 3718 Planarity : 0.004 0.066 4130 Dihedral : 13.294 141.754 3808 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.17 % Allowed : 2.42 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.16), residues: 2798 helix: 2.61 (0.12), residues: 1729 sheet: -0.05 (0.32), residues: 272 loop : -1.13 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 290 HIS 0.013 0.001 HIS D 775 PHE 0.051 0.002 PHE D 844 TYR 0.026 0.002 TYR D 995 ARG 0.010 0.000 ARG F 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9279 (mtp) cc_final: 0.8634 (mpp) REVERT: B 25 LEU cc_start: 0.9169 (mt) cc_final: 0.8894 (pp) REVERT: B 122 MET cc_start: 0.9552 (mtp) cc_final: 0.9030 (pmm) REVERT: B 144 ASN cc_start: 0.8278 (t0) cc_final: 0.8075 (t0) REVERT: B 176 LEU cc_start: 0.8596 (mt) cc_final: 0.8223 (tp) REVERT: B 288 LEU cc_start: 0.8409 (tt) cc_final: 0.8176 (pp) REVERT: B 317 MET cc_start: 0.8789 (mpp) cc_final: 0.8474 (mtm) REVERT: B 325 HIS cc_start: 0.9085 (m170) cc_final: 0.8841 (t70) REVERT: C 901 HIS cc_start: 0.8205 (p-80) cc_final: 0.7850 (p-80) REVERT: D 171 MET cc_start: 0.9133 (mtp) cc_final: 0.8906 (mtp) REVERT: F 74 TYR cc_start: 0.6480 (t80) cc_final: 0.6064 (t80) REVERT: H 95 MET cc_start: 0.1545 (ttp) cc_final: -0.0548 (mmt) outliers start: 4 outliers final: 0 residues processed: 102 average time/residue: 0.4073 time to fit residues: 65.4987 Evaluate side-chains 75 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 258 optimal weight: 0.7980 chunk 279 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS C 258 GLN C 858 GLN D 312 HIS F 69 HIS G 205 HIS H 205 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24198 Z= 0.177 Angle : 0.513 8.652 32924 Z= 0.269 Chirality : 0.038 0.243 3718 Planarity : 0.003 0.042 4130 Dihedral : 13.293 134.117 3808 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.16), residues: 2798 helix: 2.82 (0.12), residues: 1726 sheet: 0.11 (0.33), residues: 272 loop : -1.07 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 128 HIS 0.012 0.001 HIS A 163 PHE 0.030 0.001 PHE D 844 TYR 0.016 0.001 TYR C 928 ARG 0.005 0.000 ARG D1059 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9269 (mtp) cc_final: 0.8381 (mmp) REVERT: B 25 LEU cc_start: 0.9079 (mt) cc_final: 0.8843 (pp) REVERT: B 122 MET cc_start: 0.9544 (mtp) cc_final: 0.9024 (pmm) REVERT: B 144 ASN cc_start: 0.8207 (t0) cc_final: 0.7761 (t0) REVERT: B 176 LEU cc_start: 0.8472 (mt) cc_final: 0.8040 (tp) REVERT: B 288 LEU cc_start: 0.8516 (tt) cc_final: 0.8310 (pp) REVERT: B 317 MET cc_start: 0.8759 (mpp) cc_final: 0.8463 (mtm) REVERT: B 325 HIS cc_start: 0.9072 (m170) cc_final: 0.8865 (t70) REVERT: C 171 MET cc_start: 0.8477 (mtp) cc_final: 0.8136 (ttt) REVERT: C 901 HIS cc_start: 0.8280 (p-80) cc_final: 0.7939 (p-80) REVERT: D 801 MET cc_start: 0.7813 (mmm) cc_final: 0.7529 (mmt) REVERT: F 74 TYR cc_start: 0.6138 (t80) cc_final: 0.5737 (t80) REVERT: H 95 MET cc_start: 0.1603 (ttp) cc_final: 0.0220 (ttm) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.3679 time to fit residues: 55.7164 Evaluate side-chains 70 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 259 optimal weight: 40.0000 chunk 274 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 245 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 144 ASN A 159 GLN A 163 HIS ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN B 330 GLN C 775 HIS C 858 GLN ** C 944 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1022 GLN H 205 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 24198 Z= 0.403 Angle : 0.670 8.791 32924 Z= 0.350 Chirality : 0.041 0.165 3718 Planarity : 0.005 0.060 4130 Dihedral : 13.440 131.616 3808 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.16), residues: 2798 helix: 2.40 (0.12), residues: 1740 sheet: -0.09 (0.32), residues: 267 loop : -1.34 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 301 HIS 0.013 0.002 HIS A 19 PHE 0.025 0.003 PHE D 844 TYR 0.018 0.002 TYR C 181 ARG 0.008 0.001 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9285 (mtp) cc_final: 0.8891 (mpp) REVERT: A 263 MET cc_start: 0.9274 (ptp) cc_final: 0.9004 (ptm) REVERT: A 484 TYR cc_start: 0.8585 (t80) cc_final: 0.8157 (t80) REVERT: B 122 MET cc_start: 0.9574 (mtp) cc_final: 0.9082 (pmm) REVERT: B 144 ASN cc_start: 0.8265 (t0) cc_final: 0.7876 (t0) REVERT: B 176 LEU cc_start: 0.8711 (mt) cc_final: 0.8309 (tp) REVERT: B 325 HIS cc_start: 0.9022 (m170) cc_final: 0.8674 (t70) REVERT: C 171 MET cc_start: 0.8541 (mtp) cc_final: 0.8169 (ttt) REVERT: C 801 MET cc_start: 0.7268 (tpp) cc_final: 0.6958 (tpp) REVERT: D 801 MET cc_start: 0.7684 (mmm) cc_final: 0.7416 (mmp) REVERT: F 74 TYR cc_start: 0.6118 (t80) cc_final: 0.5724 (t80) REVERT: H 95 MET cc_start: 0.2257 (ttp) cc_final: 0.1227 (ttm) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.3701 time to fit residues: 53.2390 Evaluate side-chains 68 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 0.6980 chunk 246 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN C 944 HIS C 947 ASN H 205 HIS H 222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24198 Z= 0.232 Angle : 0.540 9.092 32924 Z= 0.287 Chirality : 0.038 0.142 3718 Planarity : 0.004 0.041 4130 Dihedral : 13.321 130.109 3808 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 0.04 % Allowed : 1.71 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.16), residues: 2798 helix: 2.59 (0.12), residues: 1743 sheet: -0.05 (0.32), residues: 267 loop : -1.27 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 292 HIS 0.005 0.001 HIS I 143 PHE 0.020 0.002 PHE C 242 TYR 0.012 0.001 TYR C 928 ARG 0.005 0.000 ARG D 750 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8442 (ttm) cc_final: 0.8111 (ttp) REVERT: A 122 MET cc_start: 0.9268 (mtp) cc_final: 0.8662 (mpp) REVERT: A 231 LEU cc_start: 0.8498 (tp) cc_final: 0.8170 (pp) REVERT: A 263 MET cc_start: 0.9287 (ptp) cc_final: 0.8990 (ptm) REVERT: A 484 TYR cc_start: 0.8506 (t80) cc_final: 0.8074 (t80) REVERT: B 122 MET cc_start: 0.9595 (mtp) cc_final: 0.9095 (pmm) REVERT: B 144 ASN cc_start: 0.8221 (t0) cc_final: 0.7820 (t0) REVERT: B 176 LEU cc_start: 0.8614 (mt) cc_final: 0.8130 (tp) REVERT: B 325 HIS cc_start: 0.8994 (m170) cc_final: 0.8633 (t70) REVERT: C 171 MET cc_start: 0.8468 (mtp) cc_final: 0.8084 (ttt) REVERT: C 801 MET cc_start: 0.7548 (tpp) cc_final: 0.7205 (tpp) REVERT: D 801 MET cc_start: 0.7646 (mmm) cc_final: 0.7280 (mmt) REVERT: F 74 TYR cc_start: 0.6082 (t80) cc_final: 0.5689 (t80) REVERT: H 95 MET cc_start: 0.2577 (ttp) cc_final: 0.1498 (mtm) REVERT: I 59 MET cc_start: 0.5284 (tpt) cc_final: 0.5055 (tpt) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.3792 time to fit residues: 52.9545 Evaluate side-chains 69 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 0.9990 chunk 247 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 274 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 0.0670 chunk 144 optimal weight: 1.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN C 858 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24198 Z= 0.147 Angle : 0.499 9.631 32924 Z= 0.263 Chirality : 0.037 0.143 3718 Planarity : 0.003 0.040 4130 Dihedral : 13.236 125.851 3808 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 0.04 % Allowed : 1.42 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.16), residues: 2798 helix: 2.83 (0.12), residues: 1734 sheet: 0.06 (0.33), residues: 271 loop : -1.16 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 128 HIS 0.011 0.001 HIS A 489 PHE 0.028 0.001 PHE B 336 TYR 0.015 0.001 TYR C 862 ARG 0.003 0.000 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9237 (mtp) cc_final: 0.8640 (mpp) REVERT: A 231 LEU cc_start: 0.8465 (tp) cc_final: 0.8133 (pp) REVERT: A 484 TYR cc_start: 0.8456 (t80) cc_final: 0.8060 (t80) REVERT: B 122 MET cc_start: 0.9591 (mtp) cc_final: 0.9072 (pmm) REVERT: B 144 ASN cc_start: 0.7903 (t0) cc_final: 0.7433 (t0) REVERT: B 176 LEU cc_start: 0.8594 (mt) cc_final: 0.8149 (tp) REVERT: B 288 LEU cc_start: 0.8209 (tt) cc_final: 0.7933 (pp) REVERT: B 325 HIS cc_start: 0.9017 (m170) cc_final: 0.8696 (t70) REVERT: C 801 MET cc_start: 0.7715 (tpp) cc_final: 0.7340 (tpp) REVERT: D 801 MET cc_start: 0.7634 (mmm) cc_final: 0.7298 (mmt) REVERT: F 74 TYR cc_start: 0.6052 (t80) cc_final: 0.5670 (t80) REVERT: H 95 MET cc_start: 0.2976 (ttp) cc_final: 0.1911 (mtm) REVERT: I 59 MET cc_start: 0.5344 (tpt) cc_final: 0.5049 (tpt) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.3781 time to fit residues: 52.1752 Evaluate side-chains 68 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 200 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 231 optimal weight: 0.2980 chunk 153 optimal weight: 0.9980 chunk 273 optimal weight: 9.9990 chunk 171 optimal weight: 0.0170 chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24198 Z= 0.138 Angle : 0.484 9.819 32924 Z= 0.256 Chirality : 0.037 0.137 3718 Planarity : 0.003 0.044 4130 Dihedral : 13.240 122.113 3808 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 0.04 % Allowed : 0.71 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.17), residues: 2798 helix: 2.97 (0.12), residues: 1725 sheet: 0.21 (0.33), residues: 271 loop : -1.02 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 23 HIS 0.004 0.001 HIS G 143 PHE 0.026 0.001 PHE B 336 TYR 0.009 0.001 TYR C 272 ARG 0.005 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8549 (ttm) cc_final: 0.8125 (ttp) REVERT: A 122 MET cc_start: 0.9290 (mtp) cc_final: 0.8715 (mpp) REVERT: A 185 MET cc_start: 0.8795 (mtm) cc_final: 0.8373 (mtm) REVERT: A 231 LEU cc_start: 0.8340 (tp) cc_final: 0.8031 (pp) REVERT: A 484 TYR cc_start: 0.8415 (t80) cc_final: 0.8061 (t80) REVERT: B 122 MET cc_start: 0.9583 (mtp) cc_final: 0.9063 (pmm) REVERT: B 144 ASN cc_start: 0.7827 (t0) cc_final: 0.7338 (t0) REVERT: B 176 LEU cc_start: 0.8563 (mt) cc_final: 0.8085 (tp) REVERT: B 288 LEU cc_start: 0.8130 (tt) cc_final: 0.7863 (pp) REVERT: B 325 HIS cc_start: 0.8972 (m170) cc_final: 0.8689 (t70) REVERT: C 801 MET cc_start: 0.7735 (tpp) cc_final: 0.7348 (tpp) REVERT: C 901 HIS cc_start: 0.8423 (p-80) cc_final: 0.7923 (p-80) REVERT: D 801 MET cc_start: 0.7659 (mmm) cc_final: 0.7332 (mmt) REVERT: F 74 TYR cc_start: 0.6040 (t80) cc_final: 0.5667 (t80) REVERT: H 95 MET cc_start: 0.2962 (ttp) cc_final: 0.1868 (mtm) REVERT: I 143 HIS cc_start: 0.8890 (m-70) cc_final: 0.8641 (m-70) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.3755 time to fit residues: 54.6372 Evaluate side-chains 69 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 163 optimal weight: 0.0050 chunk 82 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 174 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 249 optimal weight: 7.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24198 Z= 0.133 Angle : 0.477 9.142 32924 Z= 0.251 Chirality : 0.036 0.135 3718 Planarity : 0.003 0.040 4130 Dihedral : 13.217 118.952 3808 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.25 % Rotamer: Outliers : 0.04 % Allowed : 0.38 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.17), residues: 2798 helix: 3.02 (0.12), residues: 1725 sheet: 0.27 (0.33), residues: 278 loop : -1.06 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 128 HIS 0.004 0.001 HIS G 143 PHE 0.019 0.001 PHE C 242 TYR 0.009 0.001 TYR C 272 ARG 0.005 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.9079 (m-10) cc_final: 0.8794 (m-10) REVERT: A 60 MET cc_start: 0.8581 (ttm) cc_final: 0.8173 (ttp) REVERT: A 122 MET cc_start: 0.9275 (mtp) cc_final: 0.8697 (mpp) REVERT: A 231 LEU cc_start: 0.8322 (tp) cc_final: 0.8016 (pp) REVERT: A 484 TYR cc_start: 0.8454 (t80) cc_final: 0.8098 (t80) REVERT: B 122 MET cc_start: 0.9559 (mtp) cc_final: 0.9075 (pmm) REVERT: B 144 ASN cc_start: 0.7748 (t0) cc_final: 0.7251 (t0) REVERT: B 325 HIS cc_start: 0.8977 (m170) cc_final: 0.8715 (t70) REVERT: C 801 MET cc_start: 0.7741 (tpp) cc_final: 0.7516 (tpp) REVERT: C 901 HIS cc_start: 0.8423 (p-80) cc_final: 0.7940 (p-80) REVERT: D 801 MET cc_start: 0.7595 (mmm) cc_final: 0.7256 (mmt) REVERT: F 74 TYR cc_start: 0.6032 (t80) cc_final: 0.5667 (t80) REVERT: H 95 MET cc_start: 0.2620 (ttp) cc_final: 0.1399 (mtm) REVERT: I 59 MET cc_start: 0.5344 (tpt) cc_final: 0.4641 (tpt) REVERT: I 143 HIS cc_start: 0.8927 (m-70) cc_final: 0.8649 (m-70) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.3545 time to fit residues: 51.3458 Evaluate side-chains 69 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 9.9990 chunk 239 optimal weight: 0.4980 chunk 255 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 200 optimal weight: 0.4980 chunk 78 optimal weight: 0.3980 chunk 230 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24198 Z= 0.133 Angle : 0.475 8.739 32924 Z= 0.249 Chirality : 0.036 0.133 3718 Planarity : 0.003 0.041 4130 Dihedral : 13.166 116.813 3808 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer: Outliers : 0.04 % Allowed : 0.17 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.17), residues: 2798 helix: 3.03 (0.12), residues: 1737 sheet: 0.37 (0.33), residues: 278 loop : -1.03 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 128 HIS 0.004 0.001 HIS G 143 PHE 0.025 0.001 PHE B 336 TYR 0.012 0.001 TYR I 62 ARG 0.003 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8599 (ttm) cc_final: 0.8176 (ttp) REVERT: A 122 MET cc_start: 0.9277 (mtp) cc_final: 0.8703 (mpp) REVERT: A 231 LEU cc_start: 0.8322 (tp) cc_final: 0.8020 (pp) REVERT: A 484 TYR cc_start: 0.8433 (t80) cc_final: 0.8104 (t80) REVERT: B 122 MET cc_start: 0.9548 (mtp) cc_final: 0.9070 (pmm) REVERT: B 144 ASN cc_start: 0.7680 (t0) cc_final: 0.7181 (t0) REVERT: B 185 MET cc_start: 0.9674 (mpp) cc_final: 0.9364 (mpp) REVERT: B 325 HIS cc_start: 0.8948 (m170) cc_final: 0.8696 (t70) REVERT: C 901 HIS cc_start: 0.8428 (p-80) cc_final: 0.7948 (p-80) REVERT: D 57 MET cc_start: 0.8922 (tpp) cc_final: 0.8587 (tpp) REVERT: D 801 MET cc_start: 0.7550 (mmm) cc_final: 0.7218 (mmt) REVERT: F 74 TYR cc_start: 0.6002 (t80) cc_final: 0.5628 (t80) REVERT: H 95 MET cc_start: 0.2611 (ttp) cc_final: 0.1405 (mtm) REVERT: I 59 MET cc_start: 0.5370 (tpt) cc_final: 0.4648 (tpt) REVERT: I 143 HIS cc_start: 0.8927 (m-70) cc_final: 0.8651 (m-70) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.3530 time to fit residues: 49.4807 Evaluate side-chains 67 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 282 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS B 256 GLN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24198 Z= 0.237 Angle : 0.534 8.591 32924 Z= 0.280 Chirality : 0.038 0.150 3718 Planarity : 0.004 0.040 4130 Dihedral : 13.161 118.698 3808 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.16), residues: 2798 helix: 2.95 (0.12), residues: 1741 sheet: 0.35 (0.33), residues: 274 loop : -1.21 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 23 HIS 0.006 0.001 HIS D1069 PHE 0.017 0.002 PHE C 242 TYR 0.011 0.001 TYR I 62 ARG 0.004 0.000 ARG B 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.9124 (m-10) cc_final: 0.8870 (m-10) REVERT: A 60 MET cc_start: 0.8651 (ttm) cc_final: 0.8295 (ttp) REVERT: A 122 MET cc_start: 0.9272 (mtp) cc_final: 0.8667 (mpp) REVERT: A 484 TYR cc_start: 0.8355 (t80) cc_final: 0.8127 (t80) REVERT: B 122 MET cc_start: 0.9589 (mtp) cc_final: 0.9137 (pmm) REVERT: B 144 ASN cc_start: 0.7717 (t0) cc_final: 0.7233 (t0) REVERT: B 325 HIS cc_start: 0.8943 (m170) cc_final: 0.8665 (t70) REVERT: D 57 MET cc_start: 0.8901 (tpp) cc_final: 0.8600 (tpp) REVERT: D 801 MET cc_start: 0.7594 (mmm) cc_final: 0.7229 (mmt) REVERT: D 1055 MET cc_start: 0.9004 (mpp) cc_final: 0.8626 (mpp) REVERT: F 74 TYR cc_start: 0.6008 (t80) cc_final: 0.5643 (t80) REVERT: H 95 MET cc_start: 0.3445 (ttp) cc_final: 0.1955 (ttm) REVERT: I 59 MET cc_start: 0.5450 (tpt) cc_final: 0.4840 (tpt) REVERT: I 143 HIS cc_start: 0.8925 (m-70) cc_final: 0.8649 (m-70) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.3575 time to fit residues: 47.5268 Evaluate side-chains 64 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 225 optimal weight: 0.4980 chunk 94 optimal weight: 0.4980 chunk 231 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 198 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.075415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.049808 restraints weight = 187431.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.049136 restraints weight = 117818.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.049003 restraints weight = 76205.484| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24198 Z= 0.134 Angle : 0.483 10.239 32924 Z= 0.252 Chirality : 0.036 0.136 3718 Planarity : 0.003 0.039 4130 Dihedral : 13.085 115.450 3808 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.17), residues: 2798 helix: 3.05 (0.12), residues: 1735 sheet: 0.31 (0.33), residues: 280 loop : -1.11 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 128 HIS 0.011 0.001 HIS D 901 PHE 0.019 0.001 PHE C 242 TYR 0.012 0.001 TYR I 62 ARG 0.003 0.000 ARG A 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3838.80 seconds wall clock time: 69 minutes 59.22 seconds (4199.22 seconds total)