Starting phenix.real_space_refine on Sat Feb 7 19:45:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sod_40654/02_2026/8sod_40654_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sod_40654/02_2026/8sod_40654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sod_40654/02_2026/8sod_40654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sod_40654/02_2026/8sod_40654.map" model { file = "/net/cci-nas-00/data/ceres_data/8sod_40654/02_2026/8sod_40654_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sod_40654/02_2026/8sod_40654_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.988 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 2 5.49 5 S 107 5.16 5 C 11443 2.51 5 N 3139 2.21 5 O 3359 1.98 5 H 17995 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36045 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5118 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5118 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "A" Number of atoms: 15394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 15394 Classifications: {'peptide': 941} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 895} Chain breaks: 12 Chain: "B" Number of atoms: 8364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 8364 Classifications: {'peptide': 524} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 497} Chain breaks: 8 Chain: "F" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1012 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "D" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1012 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.36, per 1000 atoms: 0.18 Number of scatterers: 36045 At special positions: 0 Unit cell: (115.56, 142.56, 186.84, 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 107 16.00 P 2 15.00 O 3359 8.00 N 3139 7.00 C 11443 6.00 H 17995 1.00 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: 3.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4312 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 27 sheets defined 37.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.906A pdb=" N ASN E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'C' and resid 3 through 26 removed outlier: 3.876A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 36 removed outlier: 4.371A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.729A pdb=" N MET A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.775A pdb=" N TYR A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 119 through 129 removed outlier: 4.057A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 Processing helix chain 'A' and resid 171 through 180 Processing helix chain 'A' and resid 180 through 190 Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 240 through 252 Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.944A pdb=" N MET A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.614A pdb=" N LEU A 502 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 removed outlier: 3.948A pdb=" N ASP A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 560 removed outlier: 3.595A pdb=" N ALA A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 558 " --> pdb=" O GLN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 578 Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 588 through 593 Processing helix chain 'A' and resid 601 through 611 removed outlier: 3.626A pdb=" N LEU A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 639 through 649 Processing helix chain 'A' and resid 652 through 666 removed outlier: 3.627A pdb=" N TYR A 659 " --> pdb=" O ASP A 655 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN A 662 " --> pdb=" O HIS A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 686 removed outlier: 3.899A pdb=" N ARG A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 706 Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 725 through 750 Processing helix chain 'A' and resid 761 through 777 Processing helix chain 'A' and resid 797 through 801 removed outlier: 3.531A pdb=" N LYS A 800 " --> pdb=" O VAL A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 858 removed outlier: 3.794A pdb=" N LEU A 843 " --> pdb=" O ARG A 839 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 845 " --> pdb=" O ASP A 841 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 846 " --> pdb=" O MET A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 893 Processing helix chain 'A' and resid 906 through 915 Processing helix chain 'A' and resid 917 through 943 removed outlier: 4.227A pdb=" N SER A 931 " --> pdb=" O ARG A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 removed outlier: 3.651A pdb=" N LEU A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1022 Processing helix chain 'A' and resid 1023 through 1036 Processing helix chain 'A' and resid 1049 through 1056 Processing helix chain 'A' and resid 1062 through 1076 Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 39 through 51 removed outlier: 4.439A pdb=" N ASP B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 73 removed outlier: 4.214A pdb=" N LEU B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.832A pdb=" N LEU B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 118 through 136 Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 172 through 184 Processing helix chain 'B' and resid 188 through 205 removed outlier: 3.850A pdb=" N THR B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 209 removed outlier: 3.617A pdb=" N CYS B 209 " --> pdb=" O GLY B 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 209' Processing helix chain 'B' and resid 210 through 220 removed outlier: 4.132A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 240 removed outlier: 3.773A pdb=" N ALA B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.892A pdb=" N LYS B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 removed outlier: 3.600A pdb=" N GLN B 302 " --> pdb=" O PHE B 298 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 543 removed outlier: 3.900A pdb=" N LYS B 528 " --> pdb=" O ARG B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.571A pdb=" N MET B 611 " --> pdb=" O HIS B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 619 Processing helix chain 'B' and resid 650 through 663 removed outlier: 3.648A pdb=" N CYS B 660 " --> pdb=" O LEU B 656 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 705 Processing helix chain 'B' and resid 707 through 713 Processing helix chain 'B' and resid 819 through 821 No H-bonds generated for 'chain 'B' and resid 819 through 821' Processing helix chain 'F' and resid 5 through 24 Processing helix chain 'F' and resid 29 through 45 Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'D' and resid 5 through 24 removed outlier: 3.503A pdb=" N LYS D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 Processing helix chain 'D' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'E' and resid 46 through 51 removed outlier: 5.751A pdb=" N THR E 47 " --> pdb=" O ASN E 340 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN E 340 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 58 through 63 removed outlier: 3.669A pdb=" N LYS E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP E 83 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS E 89 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 100 through 105 removed outlier: 6.922A pdb=" N GLY E 115 " --> pdb=" O MET E 101 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS E 103 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA E 113 " --> pdb=" O CYS E 103 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR E 105 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR E 111 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY E 116 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE E 120 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N CYS E 121 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU E 138 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE E 123 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 134 " --> pdb=" O ASN E 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 146 through 151 removed outlier: 3.548A pdb=" N CYS E 148 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP E 170 " --> pdb=" O GLN E 176 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN E 176 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 187 through 192 removed outlier: 4.253A pdb=" N SER E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN E 220 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP E 212 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N CYS E 218 " --> pdb=" O ASP E 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 229 through 234 removed outlier: 3.696A pdb=" N ALA E 231 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS E 250 " --> pdb=" O THR E 263 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR E 263 " --> pdb=" O CYS E 250 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU E 252 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 259 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 273 through 278 removed outlier: 3.821A pdb=" N SER E 275 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP E 298 " --> pdb=" O ARG E 304 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG E 304 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.832A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.408A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.780A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.539A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.531A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.855A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.658A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 41 through 43 Processing sheet with id=AB7, first strand: chain 'A' and resid 105 through 108 Processing sheet with id=AB8, first strand: chain 'A' and resid 229 through 236 removed outlier: 7.487A pdb=" N LEU A 305 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 223 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 272 through 273 removed outlier: 4.423A pdb=" N LEU A 272 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 281 " --> pdb=" O LEU A 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 407 through 419 removed outlier: 7.658A pdb=" N VAL A 408 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASP A 369 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TRP A 410 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLY A 367 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 412 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 361 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE A 365 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU A 519 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A 367 " --> pdb=" O SER A 517 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 393 through 398 removed outlier: 4.086A pdb=" N CYS A 395 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AC4, first strand: chain 'A' and resid 783 through 784 removed outlier: 4.045A pdb=" N PHE A 783 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 793 " --> pdb=" O PHE A 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 811 through 814 Processing sheet with id=AC6, first strand: chain 'A' and resid 952 through 953 Processing sheet with id=AC7, first strand: chain 'B' and resid 288 through 292 removed outlier: 4.332A pdb=" N PHE B 520 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 683 through 685 removed outlier: 3.865A pdb=" N THR B 684 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLN B 673 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL B 832 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU B 675 " --> pdb=" O CYS B 830 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N CYS B 830 " --> pdb=" O GLU B 675 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 677 " --> pdb=" O ILE B 828 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B 826 " --> pdb=" O PHE B 812 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 812 " --> pdb=" O SER B 826 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 813 " --> pdb=" O GLY B 695 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 683 through 685 removed outlier: 3.865A pdb=" N THR B 684 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLN B 673 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL B 832 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU B 675 " --> pdb=" O CYS B 830 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N CYS B 830 " --> pdb=" O GLU B 675 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 677 " --> pdb=" O ILE B 828 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 750 " --> pdb=" O THR B 775 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 797 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 776 " --> pdb=" O SER B 793 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2265 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.08 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 17931 1.03 - 1.23: 65 1.23 - 1.42: 7642 1.42 - 1.62: 10619 1.62 - 1.81: 150 Bond restraints: 36407 Sorted by residual: bond pdb=" CD ARG A 684 " pdb=" NE ARG A 684 " ideal model delta sigma weight residual 1.458 1.438 0.020 1.40e-02 5.10e+03 2.08e+00 bond pdb=" C4 ADP A1201 " pdb=" C5 ADP A1201 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" CB GLN A 432 " pdb=" CG GLN A 432 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.43e+00 bond pdb=" CA LEU B 253 " pdb=" C LEU B 253 " ideal model delta sigma weight residual 1.519 1.507 0.012 1.22e-02 6.72e+03 1.03e+00 bond pdb=" CA TYR B 75 " pdb=" CB TYR B 75 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.58e-01 ... (remaining 36402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 65069 1.76 - 3.52: 617 3.52 - 5.28: 58 5.28 - 7.04: 6 7.04 - 8.80: 1 Bond angle restraints: 65751 Sorted by residual: angle pdb=" N LEU B 253 " pdb=" CA LEU B 253 " pdb=" C LEU B 253 " ideal model delta sigma weight residual 113.55 108.31 5.24 1.26e+00 6.30e-01 1.73e+01 angle pdb=" N ARG B 254 " pdb=" CA ARG B 254 " pdb=" C ARG B 254 " ideal model delta sigma weight residual 111.33 107.33 4.00 1.21e+00 6.83e-01 1.09e+01 angle pdb=" CA TYR B 75 " pdb=" CB TYR B 75 " pdb=" CG TYR B 75 " ideal model delta sigma weight residual 113.90 119.13 -5.23 1.80e+00 3.09e-01 8.46e+00 angle pdb=" N ARG A 927 " pdb=" CA ARG A 927 " pdb=" C ARG A 927 " ideal model delta sigma weight residual 113.19 109.77 3.42 1.19e+00 7.06e-01 8.25e+00 angle pdb=" N GLN B 45 " pdb=" CA GLN B 45 " pdb=" C GLN B 45 " ideal model delta sigma weight residual 111.82 108.62 3.20 1.16e+00 7.43e-01 7.62e+00 ... (remaining 65746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.74: 16597 29.74 - 59.47: 447 59.47 - 89.21: 30 89.21 - 118.94: 0 118.94 - 148.68: 3 Dihedral angle restraints: 17077 sinusoidal: 9317 harmonic: 7760 Sorted by residual: dihedral pdb=" CD ARG A 684 " pdb=" NE ARG A 684 " pdb=" CZ ARG A 684 " pdb=" NH1 ARG A 684 " ideal model delta sinusoidal sigma weight residual 0.00 -74.16 74.16 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" C5' ADP A1201 " pdb=" O5' ADP A1201 " pdb=" PA ADP A1201 " pdb=" O2A ADP A1201 " ideal model delta sinusoidal sigma weight residual 300.00 151.33 148.68 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" O2A ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PA ADP A1201 " pdb=" PB ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 70.00 -130.00 1 2.00e+01 2.50e-03 3.94e+01 ... (remaining 17074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1840 0.031 - 0.063: 666 0.063 - 0.094: 178 0.094 - 0.125: 119 0.125 - 0.156: 33 Chirality restraints: 2836 Sorted by residual: chirality pdb=" CA VAL B 117 " pdb=" N VAL B 117 " pdb=" C VAL B 117 " pdb=" CB VAL B 117 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA VAL E 296 " pdb=" N VAL E 296 " pdb=" C VAL E 296 " pdb=" CB VAL E 296 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE E 81 " pdb=" N ILE E 81 " pdb=" C ILE E 81 " pdb=" CB ILE E 81 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 2833 not shown) Planarity restraints: 5337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 684 " 0.965 9.50e-02 1.11e+02 3.23e-01 1.18e+02 pdb=" NE ARG A 684 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A 684 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG A 684 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG A 684 " -0.021 2.00e-02 2.50e+03 pdb="HH11 ARG A 684 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 684 " 0.016 2.00e-02 2.50e+03 pdb="HH21 ARG A 684 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 684 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 252 " -0.028 2.00e-02 2.50e+03 5.55e-02 3.08e+01 pdb=" C TRP B 252 " 0.096 2.00e-02 2.50e+03 pdb=" O TRP B 252 " -0.036 2.00e-02 2.50e+03 pdb=" N LEU B 253 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 655 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C MET B 655 " -0.058 2.00e-02 2.50e+03 pdb=" O MET B 655 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 656 " 0.020 2.00e-02 2.50e+03 ... (remaining 5334 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 500 2.06 - 2.69: 57896 2.69 - 3.33: 103652 3.33 - 3.96: 132501 3.96 - 4.60: 209237 Nonbonded interactions: 503786 Sorted by model distance: nonbonded pdb=" OD1 ASP B 131 " pdb=" HZ3 LYS B 135 " model vdw 1.421 2.450 nonbonded pdb=" HG SER E 147 " pdb=" O VAL E 187 " model vdw 1.500 2.450 nonbonded pdb=" HE ARG A 397 " pdb=" O GLU A 415 " model vdw 1.536 2.450 nonbonded pdb=" HH TYR C 264 " pdb=" O ALA C 299 " model vdw 1.541 2.450 nonbonded pdb=" HG1 THR C 274 " pdb=" O VAL C 315 " model vdw 1.554 2.450 ... (remaining 503781 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' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.240 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 34.720 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5748 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 : 0.003 0.047 18412 Z= 0.130 Angle : 0.589 8.801 24943 Z= 0.323 Chirality : 0.041 0.156 2836 Planarity : 0.009 0.416 3181 Dihedral : 13.236 148.676 6780 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.73 % Allowed : 6.36 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.16), residues: 2219 helix: -1.57 (0.17), residues: 774 sheet: -1.38 (0.22), residues: 470 loop : -2.07 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.001 ARG A 684 TYR 0.041 0.002 TYR B 658 PHE 0.021 0.002 PHE B 129 TRP 0.019 0.001 TRP B 42 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00279 (18412) covalent geometry : angle 0.58877 (24943) hydrogen bonds : bond 0.18581 ( 791) hydrogen bonds : angle 7.65121 ( 2265) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 338 time to evaluate : 1.067 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: E 45 MET cc_start: 0.0339 (tpp) cc_final: 0.0043 (mmp) REVERT: E 126 LEU cc_start: 0.5318 (mt) cc_final: 0.4978 (tt) REVERT: A 207 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7563 (tt) REVERT: A 652 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6488 (pt0) REVERT: A 878 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6907 (ptm) REVERT: A 883 LYS cc_start: 0.7985 (mttt) cc_final: 0.7758 (pttt) REVERT: A 1068 PHE cc_start: 0.5284 (t80) cc_final: 0.4858 (t80) REVERT: B 127 LEU cc_start: 0.8893 (mt) cc_final: 0.8413 (tt) REVERT: B 691 SER cc_start: 0.6860 (OUTLIER) cc_final: 0.5811 (m) outliers start: 54 outliers final: 20 residues processed: 382 average time/residue: 0.3902 time to fit residues: 208.7759 Evaluate side-chains 233 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 749 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 30.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 9 GLN E 13 GLN E 295 ASN C 259 GLN C 295 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN B 219 GLN B 295 GLN B 825 GLN F 4 ASN F 18 GLN D 4 ASN D 18 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.138432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.100358 restraints weight = 155194.482| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 3.93 r_work: 0.3941 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18412 Z= 0.192 Angle : 0.631 6.820 24943 Z= 0.334 Chirality : 0.042 0.159 2836 Planarity : 0.005 0.071 3181 Dihedral : 7.427 139.286 2496 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.47 % Allowed : 10.95 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.17), residues: 2219 helix: -0.66 (0.17), residues: 789 sheet: -1.44 (0.22), residues: 506 loop : -1.93 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 684 TYR 0.033 0.002 TYR B 658 PHE 0.019 0.002 PHE B 129 TRP 0.017 0.002 TRP A 910 HIS 0.006 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00429 (18412) covalent geometry : angle 0.63114 (24943) hydrogen bonds : bond 0.04707 ( 791) hydrogen bonds : angle 5.82075 ( 2265) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.999 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 MET cc_start: 0.2062 (tpp) cc_final: 0.1518 (mmp) REVERT: C 105 TYR cc_start: 0.3667 (OUTLIER) cc_final: 0.1189 (t80) REVERT: C 325 MET cc_start: 0.9041 (tpp) cc_final: 0.8747 (ttp) REVERT: A 207 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7651 (tt) REVERT: A 878 MET cc_start: 0.6993 (ptm) cc_final: 0.6729 (ptm) REVERT: B 71 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: B 127 LEU cc_start: 0.8901 (mt) cc_final: 0.8576 (tt) REVERT: B 164 LEU cc_start: 0.7907 (mt) cc_final: 0.7612 (tp) REVERT: B 227 GLU cc_start: 0.9120 (tt0) cc_final: 0.8909 (tm-30) REVERT: B 732 LYS cc_start: 0.7566 (tttt) cc_final: 0.7326 (tmtt) REVERT: B 771 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7801 (p) outliers start: 49 outliers final: 26 residues processed: 250 average time/residue: 0.3851 time to fit residues: 137.8221 Evaluate side-chains 217 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 60 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 20 optimal weight: 30.0000 chunk 221 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 220 GLN A 155 ASN A 386 ASN A 525 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.142952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.103681 restraints weight = 166018.335| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 4.46 r_work: 0.3877 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18412 Z= 0.196 Angle : 0.606 6.992 24943 Z= 0.321 Chirality : 0.042 0.166 2836 Planarity : 0.005 0.056 3181 Dihedral : 6.901 127.305 2474 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.47 % Allowed : 12.72 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.17), residues: 2219 helix: -0.11 (0.17), residues: 790 sheet: -1.42 (0.22), residues: 513 loop : -1.79 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 13 TYR 0.019 0.002 TYR A 124 PHE 0.020 0.002 PHE B 129 TRP 0.014 0.002 TRP A 413 HIS 0.007 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00439 (18412) covalent geometry : angle 0.60644 (24943) hydrogen bonds : bond 0.04458 ( 791) hydrogen bonds : angle 5.52800 ( 2265) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 0.931 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: 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: 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: 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: 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: symmetry clash REVERT: A 207 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7672 (tt) REVERT: A 602 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7150 (mm-30) REVERT: A 702 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7044 (mm-30) REVERT: A 878 MET cc_start: 0.7082 (ptm) cc_final: 0.6651 (ptm) REVERT: B 127 LEU cc_start: 0.8924 (mt) cc_final: 0.8547 (tt) REVERT: B 227 GLU cc_start: 0.9146 (tt0) cc_final: 0.8938 (tm-30) outliers start: 49 outliers final: 39 residues processed: 226 average time/residue: 0.3634 time to fit residues: 119.7283 Evaluate side-chains 216 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 751 VAL Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 812 PHE Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 55 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 118 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.137368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.099165 restraints weight = 154784.227| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.97 r_work: 0.3901 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18412 Z= 0.161 Angle : 0.572 6.630 24943 Z= 0.299 Chirality : 0.041 0.149 2836 Planarity : 0.004 0.056 3181 Dihedral : 6.676 124.513 2474 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.22 % Allowed : 14.44 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.17), residues: 2219 helix: 0.34 (0.18), residues: 788 sheet: -1.33 (0.22), residues: 499 loop : -1.74 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 283 TYR 0.016 0.002 TYR B 658 PHE 0.015 0.001 PHE B 129 TRP 0.018 0.001 TRP C 339 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00363 (18412) covalent geometry : angle 0.57226 (24943) hydrogen bonds : bond 0.03962 ( 791) hydrogen bonds : angle 5.23189 ( 2265) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.961 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: 0.4624 (tmm) cc_final: 0.4335 (tmm) REVERT: C 105 TYR cc_start: 0.3338 (OUTLIER) cc_final: 0.1169 (t80) REVERT: C 325 MET cc_start: 0.9047 (tpp) cc_final: 0.8791 (ttp) REVERT: A 1009 PHE cc_start: 0.7455 (t80) cc_final: 0.7240 (t80) REVERT: B 71 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: B 127 LEU cc_start: 0.8918 (mt) cc_final: 0.8549 (tt) outliers start: 44 outliers final: 36 residues processed: 217 average time/residue: 0.3418 time to fit residues: 108.9738 Evaluate side-chains 211 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 812 PHE Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 HIS C 230 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.135160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.096343 restraints weight = 157245.054| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.98 r_work: 0.3841 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 18412 Z= 0.299 Angle : 0.716 9.300 24943 Z= 0.383 Chirality : 0.045 0.188 2836 Planarity : 0.006 0.066 3181 Dihedral : 7.025 126.370 2470 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.63 % Allowed : 14.74 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.17), residues: 2219 helix: -0.35 (0.18), residues: 791 sheet: -1.50 (0.22), residues: 506 loop : -2.07 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 712 TYR 0.022 0.003 TYR B 289 PHE 0.026 0.002 PHE B 129 TRP 0.019 0.002 TRP A 413 HIS 0.008 0.002 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00675 (18412) covalent geometry : angle 0.71567 (24943) hydrogen bonds : bond 0.04963 ( 791) hydrogen bonds : angle 5.72882 ( 2265) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 178 time to evaluate : 0.946 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 MET cc_start: 0.5226 (tmm) cc_final: 0.4960 (tmm) REVERT: C 105 TYR cc_start: 0.3456 (OUTLIER) cc_final: 0.1656 (t80) REVERT: C 122 SER cc_start: 0.7025 (m) cc_final: 0.6428 (p) REVERT: A 695 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6712 (tt) REVERT: A 702 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7015 (mm-30) REVERT: A 851 MET cc_start: 0.6393 (mtp) cc_final: 0.6018 (mtp) REVERT: A 881 ILE cc_start: 0.6020 (OUTLIER) cc_final: 0.5752 (mt) REVERT: B 71 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: B 127 LEU cc_start: 0.8939 (mt) cc_final: 0.8506 (tt) outliers start: 72 outliers final: 54 residues processed: 236 average time/residue: 0.3395 time to fit residues: 117.1210 Evaluate side-chains 225 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 812 PHE Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 872 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 29 optimal weight: 50.0000 chunk 72 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.137965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.099082 restraints weight = 154316.985| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 4.06 r_work: 0.3902 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18412 Z= 0.115 Angle : 0.547 6.397 24943 Z= 0.284 Chirality : 0.041 0.188 2836 Planarity : 0.004 0.062 3181 Dihedral : 6.486 126.686 2470 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.22 % Allowed : 16.36 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.18), residues: 2219 helix: 0.64 (0.18), residues: 787 sheet: -1.40 (0.22), residues: 504 loop : -1.72 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 829 TYR 0.014 0.001 TYR B 658 PHE 0.015 0.001 PHE A 404 TRP 0.015 0.001 TRP C 339 HIS 0.003 0.001 HIS E 311 Details of bonding type rmsd covalent geometry : bond 0.00255 (18412) covalent geometry : angle 0.54657 (24943) hydrogen bonds : bond 0.03696 ( 791) hydrogen bonds : angle 5.03135 ( 2265) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.598 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 TYR cc_start: 0.3362 (OUTLIER) cc_final: 0.1472 (t80) REVERT: C 285 LEU cc_start: 0.5970 (tp) cc_final: 0.5626 (mt) REVERT: A 695 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6315 (tt) REVERT: A 702 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6805 (mm-30) REVERT: A 940 PHE cc_start: 0.8808 (t80) cc_final: 0.8595 (t80) REVERT: B 71 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: B 125 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: B 127 LEU cc_start: 0.8984 (mt) cc_final: 0.8571 (tt) outliers start: 44 outliers final: 33 residues processed: 207 average time/residue: 0.3316 time to fit residues: 101.0414 Evaluate side-chains 203 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 554 GLN Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 812 PHE Chi-restraints excluded: chain B residue 869 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 28 optimal weight: 40.0000 chunk 109 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.136831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.097809 restraints weight = 156192.521| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 4.00 r_work: 0.3862 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18412 Z= 0.182 Angle : 0.583 7.070 24943 Z= 0.307 Chirality : 0.042 0.165 2836 Planarity : 0.005 0.056 3181 Dihedral : 6.477 123.332 2468 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.62 % Allowed : 16.25 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.18), residues: 2219 helix: 0.59 (0.18), residues: 788 sheet: -1.45 (0.22), residues: 499 loop : -1.78 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.014 0.002 TYR B 658 PHE 0.013 0.001 PHE B 129 TRP 0.014 0.001 TRP A 697 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00412 (18412) covalent geometry : angle 0.58332 (24943) hydrogen bonds : bond 0.03950 ( 791) hydrogen bonds : angle 5.13884 ( 2265) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 0.694 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: 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: 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: 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: symmetry clash REVERT: C 105 TYR cc_start: 0.3393 (OUTLIER) cc_final: 0.1475 (t80) REVERT: C 285 LEU cc_start: 0.6053 (tp) cc_final: 0.5699 (mt) REVERT: A 695 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6499 (tt) REVERT: A 702 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6990 (mm-30) REVERT: A 881 ILE cc_start: 0.5867 (OUTLIER) cc_final: 0.5587 (mt) REVERT: B 71 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: B 125 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: B 127 LEU cc_start: 0.8989 (mt) cc_final: 0.8578 (tt) outliers start: 52 outliers final: 38 residues processed: 206 average time/residue: 0.3382 time to fit residues: 102.9917 Evaluate side-chains 208 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 812 PHE Chi-restraints excluded: chain B residue 869 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 148 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 212 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.136436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.097588 restraints weight = 156051.193| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 3.98 r_work: 0.3855 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18412 Z= 0.190 Angle : 0.600 7.065 24943 Z= 0.315 Chirality : 0.042 0.153 2836 Planarity : 0.005 0.058 3181 Dihedral : 6.405 122.107 2465 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.62 % Allowed : 16.20 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.18), residues: 2219 helix: 0.59 (0.18), residues: 788 sheet: -1.48 (0.22), residues: 499 loop : -1.79 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 516 TYR 0.016 0.002 TYR B 658 PHE 0.014 0.001 PHE C 292 TRP 0.013 0.002 TRP A 697 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00428 (18412) covalent geometry : angle 0.59983 (24943) hydrogen bonds : bond 0.03991 ( 791) hydrogen bonds : angle 5.14445 ( 2265) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 1.013 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 TYR cc_start: 0.3392 (OUTLIER) cc_final: 0.1467 (t80) REVERT: C 285 LEU cc_start: 0.6121 (tp) cc_final: 0.5787 (mt) REVERT: A 695 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6519 (tt) REVERT: A 881 ILE cc_start: 0.5940 (OUTLIER) cc_final: 0.5663 (mt) REVERT: A 954 ILE cc_start: 0.5308 (OUTLIER) cc_final: 0.4971 (tp) REVERT: B 71 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: B 125 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: B 127 LEU cc_start: 0.9028 (mt) cc_final: 0.8601 (tt) REVERT: B 744 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6405 (mmp) outliers start: 52 outliers final: 42 residues processed: 207 average time/residue: 0.3385 time to fit residues: 103.3920 Evaluate side-chains 213 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 635 PHE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 812 PHE Chi-restraints excluded: chain B residue 869 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 143 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 31 optimal weight: 40.0000 chunk 184 optimal weight: 7.9990 chunk 187 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 141 optimal weight: 0.6980 chunk 214 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.137542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.098659 restraints weight = 155749.121| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 4.03 r_work: 0.3871 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18412 Z= 0.119 Angle : 0.545 7.665 24943 Z= 0.281 Chirality : 0.041 0.155 2836 Planarity : 0.004 0.056 3181 Dihedral : 6.170 119.523 2465 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.07 % Allowed : 17.01 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.18), residues: 2219 helix: 1.01 (0.18), residues: 789 sheet: -1.39 (0.23), residues: 499 loop : -1.63 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.013 0.001 TYR A 100 PHE 0.013 0.001 PHE C 292 TRP 0.014 0.001 TRP A 697 HIS 0.005 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00271 (18412) covalent geometry : angle 0.54475 (24943) hydrogen bonds : bond 0.03546 ( 791) hydrogen bonds : angle 4.85278 ( 2265) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 1.103 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: C 105 TYR cc_start: 0.3844 (OUTLIER) cc_final: 0.1732 (t80) REVERT: C 285 LEU cc_start: 0.6047 (tp) cc_final: 0.5701 (mt) REVERT: C 325 MET cc_start: 0.8860 (tpp) cc_final: 0.8644 (ttp) REVERT: A 695 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6375 (tt) REVERT: A 954 ILE cc_start: 0.5115 (OUTLIER) cc_final: 0.4793 (tp) REVERT: B 71 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: B 125 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: B 127 LEU cc_start: 0.8973 (mt) cc_final: 0.8576 (tt) outliers start: 41 outliers final: 33 residues processed: 195 average time/residue: 0.3616 time to fit residues: 104.3415 Evaluate side-chains 197 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 772 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 161 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 221 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: C 220 GLN A 734 GLN ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.141843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.102046 restraints weight = 165214.674| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 4.49 r_work: 0.3858 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18412 Z= 0.146 Angle : 0.559 7.737 24943 Z= 0.290 Chirality : 0.041 0.150 2836 Planarity : 0.004 0.051 3181 Dihedral : 6.150 119.209 2465 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.97 % Allowed : 17.42 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 2219 helix: 1.02 (0.18), residues: 787 sheet: -1.39 (0.23), residues: 499 loop : -1.64 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.011 0.001 TYR B 658 PHE 0.023 0.001 PHE A 993 TRP 0.013 0.001 TRP A 697 HIS 0.005 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00332 (18412) covalent geometry : angle 0.55867 (24943) hydrogen bonds : bond 0.03631 ( 791) hydrogen bonds : angle 4.85724 ( 2265) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 1.011 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: C 105 TYR cc_start: 0.3550 (OUTLIER) cc_final: 0.1936 (t80) REVERT: C 285 LEU cc_start: 0.6274 (tp) cc_final: 0.5902 (mt) REVERT: A 695 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6357 (tt) REVERT: A 881 ILE cc_start: 0.5879 (OUTLIER) cc_final: 0.5601 (mt) REVERT: A 954 ILE cc_start: 0.5121 (OUTLIER) cc_final: 0.4779 (tp) REVERT: B 71 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: B 125 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: B 127 LEU cc_start: 0.8930 (mt) cc_final: 0.8534 (tt) outliers start: 39 outliers final: 31 residues processed: 192 average time/residue: 0.3472 time to fit residues: 99.7112 Evaluate side-chains 200 residues out of total 1981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 339 TRP Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 264 TYR Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 556 TYR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 772 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 174 optimal weight: 7.9990 chunk 172 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 41 optimal weight: 0.4980 chunk 199 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.143141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.103312 restraints weight = 163843.195| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 4.49 r_work: 0.3872 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18412 Z= 0.105 Angle : 0.527 7.614 24943 Z= 0.270 Chirality : 0.040 0.155 2836 Planarity : 0.004 0.051 3181 Dihedral : 5.907 121.907 2465 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.72 % Allowed : 17.82 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.18), residues: 2219 helix: 1.38 (0.19), residues: 788 sheet: -1.32 (0.23), residues: 499 loop : -1.51 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 146 TYR 0.013 0.001 TYR A 100 PHE 0.022 0.001 PHE A 993 TRP 0.015 0.001 TRP A 697 HIS 0.005 0.001 HIS E 311 Details of bonding type rmsd covalent geometry : bond 0.00239 (18412) covalent geometry : angle 0.52745 (24943) hydrogen bonds : bond 0.03290 ( 791) hydrogen bonds : angle 4.60750 ( 2265) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11648.80 seconds wall clock time: 197 minutes 55.42 seconds (11875.42 seconds total)