Starting phenix.real_space_refine on Fri Mar 6 19:54:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ast_11904/03_2026/7ast_11904.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ast_11904/03_2026/7ast_11904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ast_11904/03_2026/7ast_11904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ast_11904/03_2026/7ast_11904.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ast_11904/03_2026/7ast_11904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ast_11904/03_2026/7ast_11904.map" } resolution = 4.0 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= 0.001 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 236 5.16 5 C 21859 2.51 5 N 6002 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34518 Number of models: 1 Model: "" Number of chains: 17 Chain: "N" Number of atoms: 9385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1238, 9385 Classifications: {'peptide': 1238} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'CIS': 26, 'PCIS': 3, 'PTRANS': 49, 'TRANS': 1159} Chain breaks: 8 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 7, 'ARG:plan': 9, 'ASN:plan1': 4, 'GLN:plan1': 3, 'TYR:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 155 Chain: "A" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 288 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "B" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "C" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 972 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 117} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "F" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 794 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2635 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 17, 'TRANS': 311} Chain: "I" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1008 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "J" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1442 Classifications: {'peptide': 179} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 168} Chain breaks: 1 Chain: "K" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1119 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 127} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 620 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "M" Number of atoms: 8811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8811 Classifications: {'peptide': 1114} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1061} Chain: "Z" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 518 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain breaks: 2 Chain: "X" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3487 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 9, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 180 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'CIS': 4, 'TRANS': 31} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 7.34, per 1000 atoms: 0.21 Number of scatterers: 34518 At special positions: 0 Unit cell: (187.44, 146.97, 164.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 236 16.00 O 6421 8.00 N 6002 7.00 C 21859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS N 69 " - pdb=" SG CYS N 79 " distance=2.03 Simple disulfide: pdb=" SG CYS N 92 " - pdb=" SG CYS N 317 " distance=2.03 Simple disulfide: pdb=" SG CYS N 109 " - pdb=" SG CYS N 159 " distance=2.03 Simple disulfide: pdb=" SG CYS N 960 " - pdb=" SG CYS N 961 " distance=2.04 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 25 " distance=2.05 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 28 " distance=2.02 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 28 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 45 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 36 " distance=2.03 Simple disulfide: pdb=" SG CYS M1083 " - pdb=" SG CYS M1095 " distance=2.03 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: 2.91 Conformation dependent library (CDL) restraints added in 1.4 seconds 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8266 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 36 sheets defined 34.0% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'N' and resid 24 through 31 removed outlier: 4.368A pdb=" N GLN N 31 " --> pdb=" O GLU N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 105 Processing helix chain 'N' and resid 121 through 130 removed outlier: 4.396A pdb=" N PHE N 125 " --> pdb=" O GLU N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 147 removed outlier: 4.293A pdb=" N ARG N 140 " --> pdb=" O TYR N 136 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS N 145 " --> pdb=" O GLY N 141 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE N 146 " --> pdb=" O LEU N 142 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER N 147 " --> pdb=" O LYS N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 228 removed outlier: 3.920A pdb=" N VAL N 223 " --> pdb=" O ASN N 219 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 285 removed outlier: 4.137A pdb=" N LEU N 283 " --> pdb=" O THR N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 291 removed outlier: 3.636A pdb=" N ASP N 291 " --> pdb=" O ILE N 287 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 318 Processing helix chain 'N' and resid 400 through 409 removed outlier: 4.061A pdb=" N LEU N 407 " --> pdb=" O PHE N 403 " (cutoff:3.500A) Processing helix chain 'N' and resid 469 through 473 removed outlier: 3.775A pdb=" N ILE N 473 " --> pdb=" O LYS N 470 " (cutoff:3.500A) Processing helix chain 'N' and resid 489 through 493 removed outlier: 4.111A pdb=" N CYS N 493 " --> pdb=" O GLU N 490 " (cutoff:3.500A) Processing helix chain 'N' and resid 515 through 521 Processing helix chain 'N' and resid 544 through 554 Processing helix chain 'N' and resid 565 through 570 removed outlier: 3.696A pdb=" N ALA N 569 " --> pdb=" O GLN N 566 " (cutoff:3.500A) Processing helix chain 'N' and resid 597 through 602 removed outlier: 3.673A pdb=" N PHE N 601 " --> pdb=" O GLY N 597 " (cutoff:3.500A) Processing helix chain 'N' and resid 651 through 656 Processing helix chain 'N' and resid 679 through 687 Processing helix chain 'N' and resid 690 through 694 Processing helix chain 'N' and resid 710 through 734 removed outlier: 4.339A pdb=" N LEU N 716 " --> pdb=" O ALA N 712 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN N 732 " --> pdb=" O ILE N 728 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR N 733 " --> pdb=" O GLU N 729 " (cutoff:3.500A) Processing helix chain 'N' and resid 744 through 748 removed outlier: 3.622A pdb=" N THR N 747 " --> pdb=" O ALA N 744 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU N 748 " --> pdb=" O GLU N 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 744 through 748' Processing helix chain 'N' and resid 749 through 768 Processing helix chain 'N' and resid 777 through 781 Processing helix chain 'N' and resid 859 through 879 removed outlier: 5.244A pdb=" N THR N 865 " --> pdb=" O THR N 861 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA N 866 " --> pdb=" O ALA N 862 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU N 867 " --> pdb=" O VAL N 863 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY N 869 " --> pdb=" O THR N 865 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR N 870 " --> pdb=" O ALA N 866 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG N 873 " --> pdb=" O GLY N 869 " (cutoff:3.500A) Processing helix chain 'N' and resid 908 through 912 removed outlier: 3.771A pdb=" N ALA N 911 " --> pdb=" O ASP N 908 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET N 912 " --> pdb=" O PRO N 909 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 908 through 912' Processing helix chain 'N' and resid 914 through 915 No H-bonds generated for 'chain 'N' and resid 914 through 915' Processing helix chain 'N' and resid 919 through 921 No H-bonds generated for 'chain 'N' and resid 919 through 921' Processing helix chain 'N' and resid 922 through 930 removed outlier: 3.601A pdb=" N ASP N 926 " --> pdb=" O LYS N 922 " (cutoff:3.500A) Processing helix chain 'N' and resid 942 through 957 Processing helix chain 'N' and resid 967 through 992 removed outlier: 4.108A pdb=" N PHE N 972 " --> pdb=" O GLU N 968 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE N 973 " --> pdb=" O ILE N 969 " (cutoff:3.500A) Processing helix chain 'N' and resid 1001 through 1005 removed outlier: 4.067A pdb=" N ARG N1005 " --> pdb=" O GLN N1002 " (cutoff:3.500A) Processing helix chain 'N' and resid 1007 through 1025 Processing helix chain 'N' and resid 1033 through 1043 Processing helix chain 'N' and resid 1044 through 1046 No H-bonds generated for 'chain 'N' and resid 1044 through 1046' Processing helix chain 'N' and resid 1068 through 1076 removed outlier: 3.711A pdb=" N GLU N1072 " --> pdb=" O PRO N1068 " (cutoff:3.500A) Processing helix chain 'N' and resid 1094 through 1106 removed outlier: 4.399A pdb=" N VAL N1101 " --> pdb=" O TYR N1097 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU N1106 " --> pdb=" O LYS N1102 " (cutoff:3.500A) Processing helix chain 'N' and resid 1135 through 1142 removed outlier: 3.847A pdb=" N LEU N1139 " --> pdb=" O GLU N1135 " (cutoff:3.500A) Processing helix chain 'N' and resid 1145 through 1155 Processing helix chain 'N' and resid 1188 through 1194 Processing helix chain 'N' and resid 1242 through 1246 Processing helix chain 'N' and resid 1250 through 1258 removed outlier: 3.643A pdb=" N LYS N1256 " --> pdb=" O TYR N1252 " (cutoff:3.500A) Processing helix chain 'N' and resid 1259 through 1271 Processing helix chain 'N' and resid 1283 through 1295 removed outlier: 3.659A pdb=" N VAL N1287 " --> pdb=" O ASP N1283 " (cutoff:3.500A) Processing helix chain 'N' and resid 1315 through 1320 removed outlier: 3.869A pdb=" N ALA N1319 " --> pdb=" O VAL N1315 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER N1320 " --> pdb=" O LEU N1316 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 1315 through 1320' Processing helix chain 'N' and resid 1325 through 1334 removed outlier: 4.205A pdb=" N PHE N1329 " --> pdb=" O ALA N1325 " (cutoff:3.500A) Processing helix chain 'N' and resid 1343 through 1350 removed outlier: 4.202A pdb=" N ILE N1347 " --> pdb=" O VAL N1343 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE N1348 " --> pdb=" O SER N1344 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.888A pdb=" N ARG B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 removed outlier: 4.412A pdb=" N LYS B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 76 removed outlier: 4.034A pdb=" N CYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 22 removed outlier: 5.078A pdb=" N TYR F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 33 Processing helix chain 'F' and resid 36 through 45 Processing helix chain 'F' and resid 83 through 96 Processing helix chain 'F' and resid 111 through 121 Processing helix chain 'F' and resid 152 through 163 Processing helix chain 'F' and resid 178 through 183 removed outlier: 4.060A pdb=" N PHE F 183 " --> pdb=" O VAL F 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 61 removed outlier: 3.514A pdb=" N GLY G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER G 54 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 116 removed outlier: 3.581A pdb=" N ALA G 116 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 49 removed outlier: 3.545A pdb=" N PHE H 45 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS H 47 " --> pdb=" O ASP H 43 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN H 48 " --> pdb=" O ARG H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.593A pdb=" N ALA H 73 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 112 Processing helix chain 'H' and resid 158 through 163 Processing helix chain 'H' and resid 222 through 226 Processing helix chain 'H' and resid 247 through 250 removed outlier: 3.777A pdb=" N ALA H 250 " --> pdb=" O GLY H 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 247 through 250' Processing helix chain 'H' and resid 251 through 256 Processing helix chain 'H' and resid 286 through 290 removed outlier: 3.971A pdb=" N ASN H 290 " --> pdb=" O ILE H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 334 removed outlier: 3.524A pdb=" N MET H 330 " --> pdb=" O ILE H 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 28 removed outlier: 3.527A pdb=" N LYS I 28 " --> pdb=" O LYS I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 40 through 56 removed outlier: 3.830A pdb=" N THR I 44 " --> pdb=" O GLN I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 72 Processing helix chain 'I' and resid 73 through 77 removed outlier: 3.786A pdb=" N LYS I 77 " --> pdb=" O LYS I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 removed outlier: 3.698A pdb=" N LYS I 83 " --> pdb=" O THR I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 99 removed outlier: 4.155A pdb=" N ILE I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 124 removed outlier: 3.715A pdb=" N LEU I 116 " --> pdb=" O GLN I 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 18 removed outlier: 3.733A pdb=" N GLN J 17 " --> pdb=" O PRO J 14 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE J 18 " --> pdb=" O PRO J 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 14 through 18' Processing helix chain 'J' and resid 22 through 33 removed outlier: 4.080A pdb=" N LYS J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 70 removed outlier: 4.210A pdb=" N CYS K 70 " --> pdb=" O PRO K 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 67 through 70' Processing helix chain 'K' and resid 71 through 78 removed outlier: 4.060A pdb=" N ILE K 77 " --> pdb=" O LYS K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 113 removed outlier: 3.774A pdb=" N SER K 112 " --> pdb=" O SER K 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 336 removed outlier: 3.887A pdb=" N GLY L 335 " --> pdb=" O ARG L 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 28 removed outlier: 3.520A pdb=" N TRP M 27 " --> pdb=" O VAL M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 34 Processing helix chain 'M' and resid 41 through 53 Processing helix chain 'M' and resid 53 through 60 Processing helix chain 'M' and resid 235 through 243 Processing helix chain 'M' and resid 247 through 256 removed outlier: 3.601A pdb=" N ILE M 251 " --> pdb=" O SER M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 276 removed outlier: 3.636A pdb=" N MET M 262 " --> pdb=" O GLU M 258 " (cutoff:3.500A) Proline residue: M 267 - end of helix Processing helix chain 'M' and resid 284 through 289 Processing helix chain 'M' and resid 292 through 300 removed outlier: 3.556A pdb=" N MET M 296 " --> pdb=" O ARG M 293 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLY M 298 " --> pdb=" O ARG M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 314 Processing helix chain 'M' and resid 315 through 320 Processing helix chain 'M' and resid 328 through 339 Processing helix chain 'M' and resid 364 through 391 Processing helix chain 'M' and resid 410 through 422 Processing helix chain 'M' and resid 445 through 452 removed outlier: 3.658A pdb=" N MET M 452 " --> pdb=" O ALA M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 472 through 476 removed outlier: 3.990A pdb=" N GLN M 475 " --> pdb=" O GLN M 472 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP M 476 " --> pdb=" O PRO M 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 472 through 476' Processing helix chain 'M' and resid 508 through 519 removed outlier: 5.103A pdb=" N LEU M 514 " --> pdb=" O PRO M 510 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY M 519 " --> pdb=" O ALA M 515 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 526 Processing helix chain 'M' and resid 551 through 564 removed outlier: 4.677A pdb=" N ASN M 557 " --> pdb=" O LYS M 553 " (cutoff:3.500A) Processing helix chain 'M' and resid 610 through 615 Processing helix chain 'M' and resid 635 through 641 Processing helix chain 'M' and resid 660 through 664 removed outlier: 4.073A pdb=" N THR M 663 " --> pdb=" O GLU M 660 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU M 664 " --> pdb=" O PRO M 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 660 through 664' Processing helix chain 'M' and resid 679 through 693 removed outlier: 3.657A pdb=" N ASN M 683 " --> pdb=" O GLN M 679 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYS M 691 " --> pdb=" O CYS M 687 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN M 692 " --> pdb=" O ALA M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 700 through 704 Processing helix chain 'M' and resid 722 through 728 removed outlier: 3.516A pdb=" N GLU M 726 " --> pdb=" O THR M 722 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU M 727 " --> pdb=" O LYS M 723 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE M 728 " --> pdb=" O THR M 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 722 through 728' Processing helix chain 'M' and resid 912 through 916 Processing helix chain 'M' and resid 944 through 954 removed outlier: 3.983A pdb=" N LYS M 950 " --> pdb=" O LEU M 946 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU M 954 " --> pdb=" O LYS M 950 " (cutoff:3.500A) Processing helix chain 'M' and resid 968 through 979 removed outlier: 3.976A pdb=" N VAL M 972 " --> pdb=" O LYS M 968 " (cutoff:3.500A) Processing helix chain 'M' and resid 1048 through 1057 Processing helix chain 'M' and resid 1060 through 1070 Processing helix chain 'M' and resid 1107 through 1120 removed outlier: 3.885A pdb=" N LYS M1111 " --> pdb=" O PRO M1107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER M1119 " --> pdb=" O GLN M1115 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET M1120 " --> pdb=" O GLU M1116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 177 through 189 removed outlier: 3.565A pdb=" N GLN Z 183 " --> pdb=" O VAL Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 216 through 222 Processing helix chain 'Z' and resid 231 through 244 removed outlier: 4.431A pdb=" N LEU Z 242 " --> pdb=" O ILE Z 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 17 Processing helix chain 'X' and resid 18 through 32 removed outlier: 3.671A pdb=" N GLU X 22 " --> pdb=" O GLY X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 44 Processing helix chain 'X' and resid 46 through 60 Processing helix chain 'X' and resid 78 through 84 Processing helix chain 'X' and resid 86 through 99 removed outlier: 4.554A pdb=" N ARG X 90 " --> pdb=" O LEU X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 112 Processing helix chain 'X' and resid 117 through 130 Processing helix chain 'X' and resid 140 through 154 removed outlier: 3.888A pdb=" N VAL X 144 " --> pdb=" O ASP X 140 " (cutoff:3.500A) Processing helix chain 'X' and resid 238 through 259 removed outlier: 3.533A pdb=" N PHE X 242 " --> pdb=" O ASN X 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 260 through 272 removed outlier: 3.525A pdb=" N SER X 264 " --> pdb=" O ASP X 260 " (cutoff:3.500A) Processing helix chain 'X' and resid 289 through 296 Processing helix chain 'X' and resid 304 through 317 Processing helix chain 'X' and resid 337 through 357 Processing helix chain 'X' and resid 359 through 370 removed outlier: 3.506A pdb=" N ALA X 363 " --> pdb=" O GLY X 359 " (cutoff:3.500A) Processing helix chain 'X' and resid 379 through 385 removed outlier: 4.196A pdb=" N PHE X 383 " --> pdb=" O GLN X 379 " (cutoff:3.500A) Processing helix chain 'X' and resid 387 through 402 Processing helix chain 'X' and resid 427 through 456 Processing helix chain 'X' and resid 460 through 477 removed outlier: 3.791A pdb=" N ALA X 476 " --> pdb=" O ALA X 472 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR X 477 " --> pdb=" O SER X 473 " (cutoff:3.500A) Processing helix chain 'X' and resid 480 through 491 removed outlier: 3.921A pdb=" N LEU X 484 " --> pdb=" O GLU X 480 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 530 Processing helix chain 'Y' and resid 3 through 20 removed outlier: 4.224A pdb=" N UNK Y 11 " --> pdb=" O UNK Y 7 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N UNK Y 14 " --> pdb=" O UNK Y 10 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N UNK Y 20 " --> pdb=" O UNK Y 16 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 17 through 18 removed outlier: 4.022A pdb=" N HIS N 17 " --> pdb=" O LYS M1127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 164 through 166 removed outlier: 4.079A pdb=" N THR N 165 " --> pdb=" O HIS N 176 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS N 176 " --> pdb=" O THR N 165 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'N' and resid 462 through 463 removed outlier: 4.057A pdb=" N ASN N 506 " --> pdb=" O ASN N 463 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 558 through 559 Processing sheet with id=AA5, first strand: chain 'N' and resid 1215 through 1216 Processing sheet with id=AA6, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.605A pdb=" N ASN A 10 " --> pdb=" O CYS A 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 19 Processing sheet with id=AA8, first strand: chain 'C' and resid 54 through 56 removed outlier: 3.777A pdb=" N PHE C 55 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 92 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU H 142 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU H 138 " --> pdb=" O CYS H 214 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN H 139 " --> pdb=" O ILE H 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AB1, first strand: chain 'E' and resid 105 through 108 Processing sheet with id=AB2, first strand: chain 'F' and resid 81 through 82 Processing sheet with id=AB3, first strand: chain 'F' and resid 148 through 151 removed outlier: 4.108A pdb=" N VAL F 190 " --> pdb=" O MET F 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 40 through 44 removed outlier: 3.667A pdb=" N VAL G 40 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE G 84 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN G 85 " --> pdb=" O GLU G 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 60 through 66 removed outlier: 4.164A pdb=" N MET H 65 " --> pdb=" O TYR H 306 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 2 through 3 removed outlier: 3.547A pdb=" N GLU I 2 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET J 7 " --> pdb=" O PHE J 72 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE J 72 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 99 through 100 Processing sheet with id=AB8, first strand: chain 'J' and resid 106 through 107 removed outlier: 7.210A pdb=" N ASP J 106 " --> pdb=" O LEU J 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 129 through 131 removed outlier: 3.860A pdb=" N HIS J 138 " --> pdb=" O TYR J 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 124 through 125 Processing sheet with id=AC2, first strand: chain 'K' and resid 28 through 29 removed outlier: 3.787A pdb=" N ARG K 136 " --> pdb=" O CYS K 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 208 through 209 Processing sheet with id=AC4, first strand: chain 'M' and resid 169 through 171 Processing sheet with id=AC5, first strand: chain 'M' and resid 183 through 184 removed outlier: 3.813A pdb=" N GLN M 183 " --> pdb=" O ARG M 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 191 through 193 removed outlier: 3.723A pdb=" N VAL M 199 " --> pdb=" O GLU M 192 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ALA M 198 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER M 202 " --> pdb=" O ARG M 213 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG M 213 " --> pdb=" O SER M 202 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR M 214 " --> pdb=" O ARG M 226 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR M 224 " --> pdb=" O MET M 216 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 423 through 424 removed outlier: 4.192A pdb=" N ARG M 433 " --> pdb=" O TRP M 424 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 454 through 456 Processing sheet with id=AC9, first strand: chain 'M' and resid 540 through 541 removed outlier: 5.532A pdb=" N PHE M 540 " --> pdb=" O ILE M 585 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 630 through 633 removed outlier: 3.696A pdb=" N ARG M 594 " --> pdb=" O LEU M 633 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 720 through 721 Processing sheet with id=AD3, first strand: chain 'M' and resid 927 through 929 removed outlier: 8.569A pdb=" N ILE M 927 " --> pdb=" O ASN M 738 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR M 740 " --> pdb=" O ILE M 927 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N MET M 929 " --> pdb=" O THR M 740 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA M 742 " --> pdb=" O MET M 929 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 754 through 755 Processing sheet with id=AD5, first strand: chain 'M' and resid 865 through 870 removed outlier: 6.139A pdb=" N LEU M 884 " --> pdb=" O GLU M 867 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL M 869 " --> pdb=" O LYS M 882 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS M 882 " --> pdb=" O VAL M 869 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 986 through 987 Processing sheet with id=AD7, first strand: chain 'M' and resid 1075 through 1077 removed outlier: 3.619A pdb=" N PHE M1075 " --> pdb=" O ILE M1106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 34 through 35 Processing sheet with id=AD9, first strand: chain 'X' and resid 157 through 159 962 hydrogen bonds defined for protein. 2712 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: 6.10 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.62: 34734 1.62 - 2.03: 384 2.03 - 2.44: 0 2.44 - 2.85: 0 2.85 - 3.25: 2 Bond restraints: 35120 Sorted by residual: bond pdb=" CB ARG N 29 " pdb=" CG ARG N 29 " ideal model delta sigma weight residual 1.520 3.254 -1.734 3.00e-02 1.11e+03 3.34e+03 bond pdb=" CD LYS D 146 " pdb=" CE LYS D 146 " ideal model delta sigma weight residual 1.520 3.094 -1.574 3.00e-02 1.11e+03 2.75e+03 bond pdb=" CD1 PHE D 88 " pdb=" CE1 PHE D 88 " ideal model delta sigma weight residual 1.382 1.989 -0.607 3.00e-02 1.11e+03 4.10e+02 bond pdb=" CD2 PHE D 88 " pdb=" CE2 PHE D 88 " ideal model delta sigma weight residual 1.382 1.988 -0.606 3.00e-02 1.11e+03 4.07e+02 bond pdb=" CD2 TYR N 85 " pdb=" CE2 TYR N 85 " ideal model delta sigma weight residual 1.382 1.987 -0.605 3.00e-02 1.11e+03 4.07e+02 ... (remaining 35115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.02: 47230 6.02 - 12.04: 158 12.04 - 18.07: 6 18.07 - 24.09: 4 24.09 - 30.11: 1 Bond angle restraints: 47399 Sorted by residual: angle pdb=" CG LYS D 146 " pdb=" CD LYS D 146 " pdb=" CE LYS D 146 " ideal model delta sigma weight residual 111.30 141.41 -30.11 2.30e+00 1.89e-01 1.71e+02 angle pdb=" CA ARG N 29 " pdb=" CB ARG N 29 " pdb=" CG ARG N 29 " ideal model delta sigma weight residual 114.10 134.80 -20.70 2.00e+00 2.50e-01 1.07e+02 angle pdb=" CB ARG N 29 " pdb=" CG ARG N 29 " pdb=" CD ARG N 29 " ideal model delta sigma weight residual 111.30 134.41 -23.11 2.30e+00 1.89e-01 1.01e+02 angle pdb=" N PRO N 612 " pdb=" CA PRO N 612 " pdb=" CB PRO N 612 " ideal model delta sigma weight residual 103.25 111.90 -8.65 1.05e+00 9.07e-01 6.79e+01 angle pdb=" N PRO N1123 " pdb=" CA PRO N1123 " pdb=" CB PRO N1123 " ideal model delta sigma weight residual 103.34 110.40 -7.06 9.30e-01 1.16e+00 5.77e+01 ... (remaining 47394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 18779 17.78 - 35.56: 2303 35.56 - 53.35: 380 53.35 - 71.13: 49 71.13 - 88.91: 26 Dihedral angle restraints: 21537 sinusoidal: 8755 harmonic: 12782 Sorted by residual: dihedral pdb=" CA ASN N1277 " pdb=" C ASN N1277 " pdb=" N HIS N1278 " pdb=" CA HIS N1278 " ideal model delta harmonic sigma weight residual -180.00 -123.50 -56.50 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA CYS N 960 " pdb=" C CYS N 960 " pdb=" N CYS N 961 " pdb=" CA CYS N 961 " ideal model delta harmonic sigma weight residual -180.00 -124.91 -55.09 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA SER N 776 " pdb=" C SER N 776 " pdb=" N PRO N 777 " pdb=" CA PRO N 777 " ideal model delta harmonic sigma weight residual -180.00 -127.57 -52.43 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 21534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4414 0.070 - 0.140: 863 0.140 - 0.210: 87 0.210 - 0.280: 18 0.280 - 0.350: 3 Chirality restraints: 5385 Sorted by residual: chirality pdb=" CG LEU M 546 " pdb=" CB LEU M 546 " pdb=" CD1 LEU M 546 " pdb=" CD2 LEU M 546 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA LEU M 498 " pdb=" N LEU M 498 " pdb=" C LEU M 498 " pdb=" CB LEU M 498 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA PRO N1162 " pdb=" N PRO N1162 " pdb=" C PRO N1162 " pdb=" CB PRO N1162 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 5382 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG M 594 " 0.086 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PRO M 595 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO M 595 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO M 595 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU K 203 " 0.061 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO K 204 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO K 204 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO K 204 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 52 " 0.054 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO F 53 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO F 53 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 53 " 0.046 5.00e-02 4.00e+02 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 485 2.51 - 3.11: 28028 3.11 - 3.71: 54757 3.71 - 4.30: 78257 4.30 - 4.90: 122470 Nonbonded interactions: 283997 Sorted by model distance: nonbonded pdb=" SD MET N1275 " pdb=" CE MET N1280 " model vdw 1.913 3.820 nonbonded pdb=" OG1 THR B 9 " pdb=" O CYS M 924 " model vdw 1.962 3.040 nonbonded pdb=" OG SER N 817 " pdb=" O ALA N 830 " model vdw 2.041 3.040 nonbonded pdb=" O ALA H 39 " pdb=" NH2 ARG H 44 " model vdw 2.061 3.120 nonbonded pdb=" OE2 GLU M 726 " pdb=" OH TYR M 960 " model vdw 2.096 3.040 ... (remaining 283992 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 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: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.400 Find NCS groups from input model: 0.210 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4599 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 : 0.016 1.734 35130 Z= 0.582 Angle : 1.107 30.109 47419 Z= 0.595 Chirality : 0.056 0.350 5385 Planarity : 0.007 0.133 6096 Dihedral : 15.357 88.910 13241 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 32.67 Ramachandran Plot: Outliers : 0.61 % Allowed : 20.78 % Favored : 78.61 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.72 % Twisted Proline : 3.30 % Twisted General : 1.25 % 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: -4.78 (0.11), residues: 4297 helix: -1.63 (0.13), residues: 1334 sheet: -4.22 (0.27), residues: 231 loop : -4.19 (0.10), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 98 TYR 0.053 0.003 TYR M 746 PHE 0.045 0.003 PHE D 88 TRP 0.044 0.003 TRP H 40 HIS 0.014 0.002 HIS M 501 Details of bonding type rmsd covalent geometry : bond 0.01624 (35120) covalent geometry : angle 1.10219 (47399) SS BOND : bond 0.00958 ( 10) SS BOND : angle 5.06509 ( 20) hydrogen bonds : bond 0.17673 ( 962) hydrogen bonds : angle 8.06251 ( 2712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 665 time to evaluate : 1.314 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: N 307 MET cc_start: 0.0828 (tmm) cc_final: -0.0365 (tmm) REVERT: N 512 THR cc_start: 0.5926 (p) cc_final: 0.5665 (p) REVERT: N 680 MET cc_start: 0.7291 (mtm) cc_final: 0.7053 (mtp) REVERT: N 1023 MET cc_start: 0.6272 (mmm) cc_final: 0.5648 (mpp) REVERT: N 1061 MET cc_start: 0.4169 (ttm) cc_final: 0.2799 (tpt) REVERT: N 1311 MET cc_start: 0.0146 (pmm) cc_final: -0.1444 (mtt) REVERT: N 1317 MET cc_start: 0.2739 (tmm) cc_final: 0.2168 (tpt) REVERT: C 53 VAL cc_start: 0.5778 (t) cc_final: 0.5300 (t) REVERT: D 147 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7281 (pttp) REVERT: H 87 MET cc_start: 0.6655 (mmm) cc_final: 0.6386 (mmm) REVERT: I 52 TYR cc_start: 0.3448 (m-80) cc_final: 0.3212 (m-80) REVERT: J 7 MET cc_start: 0.1231 (ptm) cc_final: 0.0949 (ttp) REVERT: K 107 THR cc_start: 0.4574 (p) cc_final: 0.4255 (t) REVERT: M 136 MET cc_start: 0.5593 (tpp) cc_final: 0.5042 (mmp) REVERT: M 168 TYR cc_start: 0.7229 (p90) cc_final: 0.7016 (p90) REVERT: M 584 TYR cc_start: 0.6672 (m-80) cc_final: 0.6196 (m-80) REVERT: M 723 LYS cc_start: 0.7227 (mttt) cc_final: 0.6895 (tptt) REVERT: M 900 ARG cc_start: 0.7153 (mmt90) cc_final: 0.6760 (mtp180) REVERT: M 904 LYS cc_start: 0.7244 (ptpp) cc_final: 0.6890 (pttp) REVERT: Z 232 MET cc_start: -0.2387 (tmm) cc_final: -0.4179 (tpt) REVERT: X 385 MET cc_start: -0.0501 (ttt) cc_final: -0.3993 (mtt) REVERT: X 474 MET cc_start: -0.2866 (tmm) cc_final: -0.3485 (ttm) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 0.2519 time to fit residues: 255.8707 Evaluate side-chains 364 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.0030 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 30 GLN N 46 ASN ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 HIS N 217 ASN ** N 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 508 HIS ** N 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1075 ASN N1277 ASN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 268 GLN I 85 GLN J 115 GLN K 29 GLN M 79 ASN ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 282 GLN ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 423 ASN M 475 GLN M 535 ASN ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 738 ASN ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 806 HIS M1021 HIS M1034 GLN ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1121 ASN ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.168192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.165108 restraints weight = 84311.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.164531 restraints weight = 141950.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.164119 restraints weight = 140420.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.163932 restraints weight = 130039.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.163817 restraints weight = 120333.606| |-----------------------------------------------------------------------------| r_work (final): 0.4822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4697 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.723 35130 Z= 0.559 Angle : 0.986 25.640 47419 Z= 0.501 Chirality : 0.051 0.266 5385 Planarity : 0.007 0.111 6096 Dihedral : 8.592 55.355 4758 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 25.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 17.45 % Favored : 82.13 % Rotamer: Outliers : 1.79 % Allowed : 12.13 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.75 % Twisted Proline : 1.10 % Twisted General : 0.92 % 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: -4.37 (0.11), residues: 4297 helix: -1.30 (0.13), residues: 1345 sheet: -4.01 (0.25), residues: 283 loop : -3.90 (0.10), residues: 2669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 213 TYR 0.036 0.002 TYR M 674 PHE 0.038 0.002 PHE M 621 TRP 0.050 0.002 TRP M 297 HIS 0.013 0.002 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.01587 (35120) covalent geometry : angle 0.98447 (47399) SS BOND : bond 0.00679 ( 10) SS BOND : angle 3.13787 ( 20) hydrogen bonds : bond 0.04672 ( 962) hydrogen bonds : angle 6.27772 ( 2712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 429 time to evaluate : 1.000 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: N 680 MET cc_start: 0.7166 (mtm) cc_final: 0.6887 (mtp) REVERT: N 1039 GLN cc_start: 0.5372 (OUTLIER) cc_final: 0.4844 (mt0) REVERT: N 1061 MET cc_start: 0.4207 (ttm) cc_final: 0.3078 (tpt) REVERT: N 1311 MET cc_start: 0.0315 (pmm) cc_final: -0.1110 (mtt) REVERT: N 1317 MET cc_start: 0.2889 (tmm) cc_final: 0.2094 (tpt) REVERT: H 337 LEU cc_start: 0.6331 (tp) cc_final: 0.6086 (tt) REVERT: K 107 THR cc_start: 0.4274 (p) cc_final: 0.3889 (t) REVERT: M 684 THR cc_start: 0.7415 (p) cc_final: 0.7199 (t) REVERT: M 746 TYR cc_start: 0.5675 (OUTLIER) cc_final: 0.4564 (m-10) REVERT: M 977 VAL cc_start: 0.7100 (t) cc_final: 0.6793 (t) REVERT: Z 232 MET cc_start: -0.2547 (tmm) cc_final: -0.3724 (tpt) REVERT: X 273 MET cc_start: 0.5279 (mmm) cc_final: 0.5077 (mmm) REVERT: X 385 MET cc_start: -0.0217 (ttt) cc_final: -0.3557 (mtt) REVERT: X 474 MET cc_start: -0.3026 (tmm) cc_final: -0.3456 (ttm) outliers start: 67 outliers final: 27 residues processed: 465 average time/residue: 0.2221 time to fit residues: 163.0273 Evaluate side-chains 373 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 344 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1227 VAL Chi-restraints excluded: chain N residue 1280 MET Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 268 GLN Chi-restraints excluded: chain H residue 284 SER Chi-restraints excluded: chain H residue 334 ARG Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 79 ASN Chi-restraints excluded: chain M residue 148 THR Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 432 ASP Chi-restraints excluded: chain M residue 475 GLN Chi-restraints excluded: chain M residue 503 THR Chi-restraints excluded: chain M residue 665 LEU Chi-restraints excluded: chain M residue 674 TYR Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 938 MET Chi-restraints excluded: chain M residue 1050 MET Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 26 optimal weight: 10.0000 chunk 286 optimal weight: 0.7980 chunk 373 optimal weight: 8.9990 chunk 424 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 218 optimal weight: 50.0000 chunk 109 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 221 optimal weight: 0.0970 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 662 ASN ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 138 ASN ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 GLN ** H 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 GLN ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 ASN M 208 HIS ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 642 ASN ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 ASN X 445 ASN X 497 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.167602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.165363 restraints weight = 84325.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.165028 restraints weight = 127415.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.164800 restraints weight = 133610.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.164526 restraints weight = 124559.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.164352 restraints weight = 142036.457| |-----------------------------------------------------------------------------| r_work (final): 0.4824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4709 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.725 35130 Z= 0.556 Angle : 0.924 24.134 47419 Z= 0.467 Chirality : 0.049 0.248 5385 Planarity : 0.006 0.091 6096 Dihedral : 8.102 54.824 4758 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.35 % Allowed : 17.10 % Favored : 82.55 % Rotamer: Outliers : 2.35 % Allowed : 15.22 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.77 % Twisted Proline : 1.10 % Twisted General : 0.75 % 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: -4.09 (0.12), residues: 4297 helix: -1.08 (0.14), residues: 1344 sheet: -3.53 (0.27), residues: 275 loop : -3.75 (0.10), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 31 TYR 0.043 0.002 TYR I 47 PHE 0.035 0.002 PHE M 91 TRP 0.028 0.002 TRP M 297 HIS 0.009 0.001 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.01583 (35120) covalent geometry : angle 0.92189 (47399) SS BOND : bond 0.00664 ( 10) SS BOND : angle 2.87378 ( 20) hydrogen bonds : bond 0.04110 ( 962) hydrogen bonds : angle 5.86423 ( 2712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 372 time to evaluate : 1.453 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: N 1023 MET cc_start: 0.6756 (mmt) cc_final: 0.6278 (mmp) REVERT: N 1039 GLN cc_start: 0.5128 (OUTLIER) cc_final: 0.4424 (mt0) REVERT: N 1061 MET cc_start: 0.4503 (ttm) cc_final: 0.3369 (tpt) REVERT: N 1311 MET cc_start: 0.0388 (pmm) cc_final: -0.1109 (mtt) REVERT: N 1317 MET cc_start: 0.2841 (tmm) cc_final: 0.2231 (tpt) REVERT: B 52 HIS cc_start: 0.7571 (OUTLIER) cc_final: 0.7053 (t-90) REVERT: H 68 ILE cc_start: 0.6615 (OUTLIER) cc_final: 0.6376 (pt) REVERT: K 114 TYR cc_start: 0.4863 (OUTLIER) cc_final: 0.3999 (m-80) REVERT: M 47 PHE cc_start: 0.7265 (t80) cc_final: 0.6991 (t80) REVERT: M 168 TYR cc_start: 0.7452 (p90) cc_final: 0.7130 (p90) REVERT: M 746 TYR cc_start: 0.5567 (OUTLIER) cc_final: 0.4299 (m-10) REVERT: M 929 MET cc_start: 0.6479 (mtp) cc_final: 0.6192 (mtt) REVERT: M 977 VAL cc_start: 0.7040 (t) cc_final: 0.6601 (t) REVERT: M 979 HIS cc_start: 0.5704 (OUTLIER) cc_final: 0.5281 (m90) REVERT: Z 232 MET cc_start: -0.2426 (tmm) cc_final: -0.3688 (tpt) REVERT: X 385 MET cc_start: 0.0306 (ttt) cc_final: -0.3360 (mtt) REVERT: X 474 MET cc_start: -0.3309 (tmm) cc_final: -0.3769 (ttm) outliers start: 88 outliers final: 42 residues processed: 437 average time/residue: 0.2186 time to fit residues: 156.2526 Evaluate side-chains 369 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 321 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 22 MET Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1247 THR Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 284 SER Chi-restraints excluded: chain H residue 334 ARG Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 445 TYR Chi-restraints excluded: chain M residue 499 MET Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 665 LEU Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 895 ASP Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 938 MET Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 154 optimal weight: 9.9990 chunk 225 optimal weight: 50.0000 chunk 57 optimal weight: 0.7980 chunk 138 optimal weight: 0.0060 chunk 194 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 431 optimal weight: 50.0000 chunk 298 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 299 optimal weight: 0.8980 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1026 GLN ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 GLN K 110 ASN L 358 GLN M 79 ASN ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 410 GLN ** M 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 49 GLN X 238 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.166566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.164466 restraints weight = 83674.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.164259 restraints weight = 124416.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.164028 restraints weight = 134161.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.163842 restraints weight = 117649.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.163832 restraints weight = 113097.412| |-----------------------------------------------------------------------------| r_work (final): 0.4817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4749 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.724 35130 Z= 0.556 Angle : 0.903 23.501 47419 Z= 0.458 Chirality : 0.049 0.268 5385 Planarity : 0.006 0.086 6096 Dihedral : 7.783 54.683 4758 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.40 % Allowed : 17.08 % Favored : 82.52 % Rotamer: Outliers : 3.18 % Allowed : 17.20 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.58 % 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: -3.88 (0.12), residues: 4297 helix: -0.87 (0.14), residues: 1345 sheet: -3.44 (0.27), residues: 297 loop : -3.63 (0.11), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 292 TYR 0.042 0.002 TYR I 47 PHE 0.038 0.002 PHE M 91 TRP 0.028 0.002 TRP M 297 HIS 0.010 0.001 HIS M 676 Details of bonding type rmsd covalent geometry : bond 0.01584 (35120) covalent geometry : angle 0.90108 (47399) SS BOND : bond 0.00685 ( 10) SS BOND : angle 2.84760 ( 20) hydrogen bonds : bond 0.03893 ( 962) hydrogen bonds : angle 5.62247 ( 2712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 363 time to evaluate : 1.199 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: N 731 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6501 (tt) REVERT: N 1023 MET cc_start: 0.6276 (mmt) cc_final: 0.5881 (mmp) REVERT: N 1039 GLN cc_start: 0.5118 (OUTLIER) cc_final: 0.4352 (mt0) REVERT: N 1311 MET cc_start: 0.0223 (pmm) cc_final: -0.1183 (mtt) REVERT: N 1317 MET cc_start: 0.2858 (tmm) cc_final: 0.2251 (tpt) REVERT: B 42 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6670 (mtm180) REVERT: B 52 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.7134 (t-90) REVERT: F 133 GLN cc_start: 0.4546 (OUTLIER) cc_final: 0.4342 (mm-40) REVERT: G 45 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7623 (m170) REVERT: J 76 VAL cc_start: 0.4142 (OUTLIER) cc_final: 0.2091 (m) REVERT: K 114 TYR cc_start: 0.4647 (OUTLIER) cc_final: 0.4060 (m-80) REVERT: M 47 PHE cc_start: 0.7491 (t80) cc_final: 0.7031 (t80) REVERT: M 143 SER cc_start: 0.7496 (p) cc_final: 0.7223 (t) REVERT: M 168 TYR cc_start: 0.7645 (p90) cc_final: 0.7372 (p90) REVERT: M 546 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5902 (tt) REVERT: M 692 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.6319 (pt0) REVERT: M 744 MET cc_start: 0.6695 (mmm) cc_final: 0.6430 (mmm) REVERT: M 746 TYR cc_start: 0.5655 (OUTLIER) cc_final: 0.4254 (m-10) REVERT: M 759 LYS cc_start: 0.6073 (ptpt) cc_final: 0.5658 (pttt) REVERT: M 929 MET cc_start: 0.6693 (mtp) cc_final: 0.6392 (mtt) REVERT: M 979 HIS cc_start: 0.5726 (OUTLIER) cc_final: 0.5102 (m90) REVERT: Z 232 MET cc_start: -0.2310 (tmm) cc_final: -0.3390 (tpt) REVERT: X 139 MET cc_start: -0.1538 (tmm) cc_final: -0.1753 (ttt) REVERT: X 385 MET cc_start: 0.0145 (ttt) cc_final: -0.3662 (mtt) REVERT: X 474 MET cc_start: -0.3468 (tmm) cc_final: -0.3676 (ttm) outliers start: 119 outliers final: 46 residues processed: 460 average time/residue: 0.2094 time to fit residues: 157.6536 Evaluate side-chains 372 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 314 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 479 ARG Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1247 THR Chi-restraints excluded: chain N residue 1280 MET Chi-restraints excluded: chain N residue 1359 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 45 HIS Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 143 GLN Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 284 SER Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 79 ASN Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 236 ILE Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 445 TYR Chi-restraints excluded: chain M residue 498 LEU Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 546 LEU Chi-restraints excluded: chain M residue 665 LEU Chi-restraints excluded: chain M residue 692 GLN Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 828 VAL Chi-restraints excluded: chain M residue 857 THR Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 938 MET Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 88 optimal weight: 10.0000 chunk 242 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 99 optimal weight: 9.9990 chunk 317 optimal weight: 0.0970 chunk 43 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 374 ASN ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 802 GLN ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 ASN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN ** K 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.172707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.167978 restraints weight = 79652.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.167636 restraints weight = 146674.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.167449 restraints weight = 156542.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.167078 restraints weight = 124781.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.166953 restraints weight = 137334.124| |-----------------------------------------------------------------------------| r_work (final): 0.4802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4908 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.725 35130 Z= 0.559 Angle : 0.901 23.263 47419 Z= 0.454 Chirality : 0.049 0.268 5385 Planarity : 0.006 0.089 6096 Dihedral : 7.675 54.498 4758 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 23.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 16.92 % Favored : 82.73 % Rotamer: Outliers : 2.94 % Allowed : 19.82 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.55 % 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: -3.82 (0.12), residues: 4297 helix: -0.82 (0.14), residues: 1357 sheet: -3.62 (0.25), residues: 326 loop : -3.57 (0.11), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 800 TYR 0.036 0.002 TYR I 47 PHE 0.048 0.002 PHE M 91 TRP 0.019 0.002 TRP M 297 HIS 0.013 0.001 HIS J 78 Details of bonding type rmsd covalent geometry : bond 0.01591 (35120) covalent geometry : angle 0.89979 (47399) SS BOND : bond 0.00648 ( 10) SS BOND : angle 2.70826 ( 20) hydrogen bonds : bond 0.03851 ( 962) hydrogen bonds : angle 5.52867 ( 2712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 338 time to evaluate : 1.128 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: N 674 ASN cc_start: 0.6183 (t0) cc_final: 0.5919 (t0) REVERT: N 731 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6443 (tt) REVERT: N 1023 MET cc_start: 0.6355 (mmt) cc_final: 0.5851 (mmp) REVERT: N 1039 GLN cc_start: 0.5279 (OUTLIER) cc_final: 0.4468 (mt0) REVERT: N 1311 MET cc_start: 0.0328 (pmm) cc_final: -0.1149 (mtt) REVERT: N 1317 MET cc_start: 0.3187 (tmm) cc_final: 0.2343 (tpt) REVERT: B 52 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.7035 (t-90) REVERT: B 62 TYR cc_start: 0.6481 (p90) cc_final: 0.5203 (p90) REVERT: F 133 GLN cc_start: 0.4842 (OUTLIER) cc_final: 0.4473 (mm-40) REVERT: G 45 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.7609 (m170) REVERT: G 70 TYR cc_start: 0.7991 (t80) cc_final: 0.7742 (t80) REVERT: H 198 LEU cc_start: 0.5985 (tp) cc_final: 0.5721 (tp) REVERT: H 330 MET cc_start: 0.7932 (mmm) cc_final: 0.6521 (mtp) REVERT: K 114 TYR cc_start: 0.4698 (OUTLIER) cc_final: 0.4151 (m-80) REVERT: M 47 PHE cc_start: 0.7500 (t80) cc_final: 0.7048 (t80) REVERT: M 168 TYR cc_start: 0.7746 (p90) cc_final: 0.7483 (p90) REVERT: M 676 HIS cc_start: 0.6475 (OUTLIER) cc_final: 0.6083 (m-70) REVERT: M 692 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6416 (pt0) REVERT: M 746 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.4525 (m-10) REVERT: M 929 MET cc_start: 0.6768 (mtp) cc_final: 0.6479 (mtt) REVERT: M 979 HIS cc_start: 0.5695 (OUTLIER) cc_final: 0.5015 (m90) REVERT: Z 232 MET cc_start: -0.2501 (tmm) cc_final: -0.3592 (tpt) REVERT: X 385 MET cc_start: 0.0274 (ttt) cc_final: -0.3893 (mtt) outliers start: 110 outliers final: 63 residues processed: 428 average time/residue: 0.2050 time to fit residues: 145.6841 Evaluate side-chains 380 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 307 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 22 MET Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 479 ARG Chi-restraints excluded: chain N residue 560 ASP Chi-restraints excluded: chain N residue 567 ILE Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 809 VAL Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1064 THR Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1280 MET Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 45 HIS Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 284 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 445 TYR Chi-restraints excluded: chain M residue 498 LEU Chi-restraints excluded: chain M residue 503 THR Chi-restraints excluded: chain M residue 542 ASN Chi-restraints excluded: chain M residue 665 LEU Chi-restraints excluded: chain M residue 676 HIS Chi-restraints excluded: chain M residue 692 GLN Chi-restraints excluded: chain M residue 712 LEU Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 822 GLU Chi-restraints excluded: chain M residue 828 VAL Chi-restraints excluded: chain M residue 857 THR Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 938 MET Chi-restraints excluded: chain M residue 958 PHE Chi-restraints excluded: chain M residue 977 VAL Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain Z residue 218 LYS Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 115 optimal weight: 7.9990 chunk 285 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 chunk 351 optimal weight: 0.0470 chunk 21 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 403 optimal weight: 50.0000 chunk 256 optimal weight: 7.9990 overall best weight: 1.2280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 HIS F 43 GLN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 201 GLN J 31 ASN J 78 HIS ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 501 HIS ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 610 HIS ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 903 GLN ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 497 GLN X 507 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.173967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.168323 restraints weight = 79868.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.167801 restraints weight = 129083.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.167281 restraints weight = 148231.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.166881 restraints weight = 130707.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.166632 restraints weight = 148309.585| |-----------------------------------------------------------------------------| r_work (final): 0.4790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4942 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.724 35130 Z= 0.552 Angle : 0.881 23.325 47419 Z= 0.442 Chirality : 0.048 0.258 5385 Planarity : 0.006 0.085 6096 Dihedral : 7.462 54.207 4758 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.37 % Allowed : 16.15 % Favored : 83.48 % Rotamer: Outliers : 3.29 % Allowed : 20.75 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.43 % 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: -3.70 (0.12), residues: 4297 helix: -0.73 (0.14), residues: 1363 sheet: -3.45 (0.25), residues: 331 loop : -3.50 (0.11), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 800 TYR 0.032 0.002 TYR I 47 PHE 0.038 0.002 PHE M 91 TRP 0.018 0.001 TRP M 297 HIS 0.012 0.001 HIS J 78 Details of bonding type rmsd covalent geometry : bond 0.01579 (35120) covalent geometry : angle 0.87990 (47399) SS BOND : bond 0.00641 ( 10) SS BOND : angle 2.60309 ( 20) hydrogen bonds : bond 0.03752 ( 962) hydrogen bonds : angle 5.40402 ( 2712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 335 time to evaluate : 1.331 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: N 731 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6523 (tt) REVERT: N 1023 MET cc_start: 0.5819 (mmt) cc_final: 0.5614 (mmp) REVERT: N 1039 GLN cc_start: 0.5303 (OUTLIER) cc_final: 0.4443 (mt0) REVERT: N 1311 MET cc_start: 0.0211 (pmm) cc_final: -0.1235 (mtt) REVERT: N 1317 MET cc_start: 0.3067 (tmm) cc_final: 0.2274 (tpt) REVERT: B 52 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.7082 (t-90) REVERT: F 133 GLN cc_start: 0.5004 (OUTLIER) cc_final: 0.4611 (mm-40) REVERT: G 79 LYS cc_start: 0.8538 (tmtt) cc_final: 0.8168 (tmtt) REVERT: H 198 LEU cc_start: 0.6101 (tp) cc_final: 0.5868 (tp) REVERT: H 330 MET cc_start: 0.7904 (mmm) cc_final: 0.6693 (mtp) REVERT: K 114 TYR cc_start: 0.3909 (OUTLIER) cc_final: 0.3614 (m-80) REVERT: M 168 TYR cc_start: 0.7753 (p90) cc_final: 0.7512 (p90) REVERT: M 377 PHE cc_start: 0.4427 (m-10) cc_final: 0.3638 (m-80) REVERT: M 546 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6178 (tt) REVERT: M 676 HIS cc_start: 0.6412 (OUTLIER) cc_final: 0.5937 (m-70) REVERT: M 746 TYR cc_start: 0.5811 (OUTLIER) cc_final: 0.4568 (m-10) REVERT: M 929 MET cc_start: 0.6824 (mtp) cc_final: 0.6602 (mtp) REVERT: M 979 HIS cc_start: 0.5816 (OUTLIER) cc_final: 0.5055 (m90) REVERT: M 1004 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8020 (t80) REVERT: M 1069 MET cc_start: 0.6827 (ppp) cc_final: 0.6084 (ppp) REVERT: Z 232 MET cc_start: -0.2579 (tmm) cc_final: -0.3506 (tpt) REVERT: X 385 MET cc_start: 0.0519 (ttt) cc_final: -0.4213 (mtt) REVERT: X 531 MET cc_start: 0.2448 (mmm) cc_final: 0.1860 (tpt) outliers start: 123 outliers final: 65 residues processed: 435 average time/residue: 0.2053 time to fit residues: 147.2037 Evaluate side-chains 386 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 311 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 479 ARG Chi-restraints excluded: chain N residue 560 ASP Chi-restraints excluded: chain N residue 581 VAL Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 809 VAL Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 953 MET Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1064 THR Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1280 MET Chi-restraints excluded: chain N residue 1359 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 445 TYR Chi-restraints excluded: chain M residue 498 LEU Chi-restraints excluded: chain M residue 503 THR Chi-restraints excluded: chain M residue 542 ASN Chi-restraints excluded: chain M residue 546 LEU Chi-restraints excluded: chain M residue 665 LEU Chi-restraints excluded: chain M residue 676 HIS Chi-restraints excluded: chain M residue 712 LEU Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 804 TRP Chi-restraints excluded: chain M residue 822 GLU Chi-restraints excluded: chain M residue 857 THR Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 895 ASP Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 938 MET Chi-restraints excluded: chain M residue 958 PHE Chi-restraints excluded: chain M residue 977 VAL Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain M residue 1004 PHE Chi-restraints excluded: chain M residue 1016 VAL Chi-restraints excluded: chain Z residue 218 LYS Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 163 optimal weight: 6.9990 chunk 400 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 426 optimal weight: 30.0000 chunk 415 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 375 optimal weight: 7.9990 chunk 263 optimal weight: 0.8980 chunk 417 optimal weight: 4.9990 chunk 274 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 508 HIS ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN M 92 ASN ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 552 HIS ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 703 ASN ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 913 GLN ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 497 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.172954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.167613 restraints weight = 80231.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.166791 restraints weight = 142949.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.166425 restraints weight = 163626.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.165943 restraints weight = 141775.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.165726 restraints weight = 149736.402| |-----------------------------------------------------------------------------| r_work (final): 0.4768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5005 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.726 35130 Z= 0.560 Angle : 0.908 23.002 47419 Z= 0.455 Chirality : 0.049 0.263 5385 Planarity : 0.006 0.092 6096 Dihedral : 7.479 54.099 4758 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.35 % Allowed : 16.48 % Favored : 83.17 % Rotamer: Outliers : 3.12 % Allowed : 21.69 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.41 % 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: -3.66 (0.12), residues: 4297 helix: -0.71 (0.14), residues: 1367 sheet: -3.51 (0.24), residues: 357 loop : -3.45 (0.11), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 310 TYR 0.028 0.002 TYR M 674 PHE 0.041 0.002 PHE M 91 TRP 0.021 0.002 TRP M 804 HIS 0.008 0.001 HIS N1239 Details of bonding type rmsd covalent geometry : bond 0.01595 (35120) covalent geometry : angle 0.90693 (47399) SS BOND : bond 0.00615 ( 10) SS BOND : angle 2.54371 ( 20) hydrogen bonds : bond 0.03831 ( 962) hydrogen bonds : angle 5.41937 ( 2712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 326 time to evaluate : 1.306 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: N 731 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6627 (tt) REVERT: N 1039 GLN cc_start: 0.5329 (OUTLIER) cc_final: 0.4312 (mt0) REVERT: N 1311 MET cc_start: 0.0180 (pmm) cc_final: -0.1261 (mtt) REVERT: N 1317 MET cc_start: 0.3316 (tmm) cc_final: 0.2391 (tpt) REVERT: B 48 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7548 (mtm) REVERT: B 52 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.7103 (t-90) REVERT: F 133 GLN cc_start: 0.5391 (OUTLIER) cc_final: 0.4811 (mm-40) REVERT: G 58 MET cc_start: 0.5705 (mmm) cc_final: 0.5489 (mmm) REVERT: H 330 MET cc_start: 0.7916 (mmm) cc_final: 0.7213 (mtp) REVERT: K 114 TYR cc_start: 0.4214 (OUTLIER) cc_final: 0.3847 (m-80) REVERT: M 168 TYR cc_start: 0.7673 (p90) cc_final: 0.7412 (p90) REVERT: M 377 PHE cc_start: 0.4368 (m-10) cc_final: 0.3535 (m-80) REVERT: M 546 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6056 (tt) REVERT: M 676 HIS cc_start: 0.6452 (OUTLIER) cc_final: 0.6041 (m-70) REVERT: M 746 TYR cc_start: 0.5808 (OUTLIER) cc_final: 0.4503 (m-10) REVERT: M 825 GLN cc_start: 0.8420 (mt0) cc_final: 0.8091 (mt0) REVERT: M 979 HIS cc_start: 0.5974 (OUTLIER) cc_final: 0.5650 (m-70) REVERT: M 1004 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8050 (t80) REVERT: M 1069 MET cc_start: 0.6884 (ppp) cc_final: 0.6488 (ppp) REVERT: Z 232 MET cc_start: -0.2544 (tmm) cc_final: -0.3205 (tpt) REVERT: X 385 MET cc_start: -0.0135 (ttt) cc_final: -0.4538 (mtt) outliers start: 117 outliers final: 75 residues processed: 425 average time/residue: 0.2047 time to fit residues: 143.1592 Evaluate side-chains 396 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 310 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 265 SER Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 428 MET Chi-restraints excluded: chain N residue 479 ARG Chi-restraints excluded: chain N residue 483 HIS Chi-restraints excluded: chain N residue 567 ILE Chi-restraints excluded: chain N residue 581 VAL Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 809 VAL Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 1039 GLN Chi-restraints excluded: chain N residue 1064 THR Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1280 MET Chi-restraints excluded: chain N residue 1343 VAL Chi-restraints excluded: chain N residue 1359 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 143 GLN Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 312 LEU Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 319 THR Chi-restraints excluded: chain M residue 445 TYR Chi-restraints excluded: chain M residue 498 LEU Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 542 ASN Chi-restraints excluded: chain M residue 546 LEU Chi-restraints excluded: chain M residue 665 LEU Chi-restraints excluded: chain M residue 676 HIS Chi-restraints excluded: chain M residue 712 LEU Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 759 LYS Chi-restraints excluded: chain M residue 822 GLU Chi-restraints excluded: chain M residue 828 VAL Chi-restraints excluded: chain M residue 857 THR Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 895 ASP Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 938 MET Chi-restraints excluded: chain M residue 958 PHE Chi-restraints excluded: chain M residue 977 VAL Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain M residue 1004 PHE Chi-restraints excluded: chain M residue 1086 LEU Chi-restraints excluded: chain Z residue 218 LYS Chi-restraints excluded: chain X residue 146 ASN Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 23 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 180 optimal weight: 0.8980 chunk 277 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 221 optimal weight: 40.0000 chunk 144 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 307 optimal weight: 2.9990 chunk 226 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.175997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.171129 restraints weight = 81810.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.170443 restraints weight = 141036.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.170070 restraints weight = 153998.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.169541 restraints weight = 153290.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.169448 restraints weight = 150040.647| |-----------------------------------------------------------------------------| r_work (final): 0.4780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4985 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.727 35130 Z= 0.556 Angle : 0.896 23.018 47419 Z= 0.446 Chirality : 0.048 0.257 5385 Planarity : 0.006 0.101 6096 Dihedral : 7.407 54.801 4758 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.33 % Allowed : 16.66 % Favored : 83.01 % Rotamer: Outliers : 2.91 % Allowed : 21.98 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.39 % 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: -3.59 (0.12), residues: 4297 helix: -0.63 (0.14), residues: 1359 sheet: -3.54 (0.24), residues: 355 loop : -3.40 (0.11), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 889 TYR 0.028 0.002 TYR I 47 PHE 0.048 0.002 PHE M 50 TRP 0.057 0.002 TRP H 40 HIS 0.008 0.001 HIS N1239 Details of bonding type rmsd covalent geometry : bond 0.01587 (35120) covalent geometry : angle 0.89491 (47399) SS BOND : bond 0.00608 ( 10) SS BOND : angle 2.50816 ( 20) hydrogen bonds : bond 0.03743 ( 962) hydrogen bonds : angle 5.36270 ( 2712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 316 time to evaluate : 1.503 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: N 731 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6535 (tt) REVERT: N 1311 MET cc_start: 0.0150 (pmm) cc_final: -0.1286 (mtt) REVERT: N 1317 MET cc_start: 0.3225 (tmm) cc_final: 0.2369 (tpt) REVERT: B 48 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7610 (mtm) REVERT: B 52 HIS cc_start: 0.7838 (OUTLIER) cc_final: 0.7167 (t-90) REVERT: F 133 GLN cc_start: 0.5610 (OUTLIER) cc_final: 0.4966 (mm-40) REVERT: H 198 LEU cc_start: 0.6259 (tp) cc_final: 0.5988 (tp) REVERT: H 330 MET cc_start: 0.7813 (mmm) cc_final: 0.7133 (mtp) REVERT: K 114 TYR cc_start: 0.4157 (OUTLIER) cc_final: 0.3827 (m-80) REVERT: M 168 TYR cc_start: 0.7697 (p90) cc_final: 0.7392 (p90) REVERT: M 377 PHE cc_start: 0.4391 (m-10) cc_final: 0.3565 (m-80) REVERT: M 546 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6029 (tt) REVERT: M 621 PHE cc_start: 0.4979 (t80) cc_final: 0.4648 (t80) REVERT: M 676 HIS cc_start: 0.6396 (OUTLIER) cc_final: 0.5923 (m-70) REVERT: M 746 TYR cc_start: 0.5938 (OUTLIER) cc_final: 0.4654 (m-10) REVERT: M 825 GLN cc_start: 0.8390 (mt0) cc_final: 0.8136 (mt0) REVERT: M 979 HIS cc_start: 0.5765 (OUTLIER) cc_final: 0.5446 (m-70) REVERT: M 1004 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.8004 (t80) REVERT: M 1069 MET cc_start: 0.6838 (ppp) cc_final: 0.6295 (ppp) REVERT: Z 232 MET cc_start: -0.2610 (tmm) cc_final: -0.3251 (tpt) REVERT: X 385 MET cc_start: 0.0006 (ttt) cc_final: -0.4733 (mtt) REVERT: X 434 MET cc_start: -0.0569 (ttp) cc_final: -0.1012 (ttp) outliers start: 109 outliers final: 83 residues processed: 403 average time/residue: 0.2067 time to fit residues: 138.2402 Evaluate side-chains 394 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 301 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 428 MET Chi-restraints excluded: chain N residue 483 HIS Chi-restraints excluded: chain N residue 507 LEU Chi-restraints excluded: chain N residue 560 ASP Chi-restraints excluded: chain N residue 567 ILE Chi-restraints excluded: chain N residue 581 VAL Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 758 VAL Chi-restraints excluded: chain N residue 809 VAL Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 946 ILE Chi-restraints excluded: chain N residue 1064 THR Chi-restraints excluded: chain N residue 1082 THR Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1280 MET Chi-restraints excluded: chain N residue 1343 VAL Chi-restraints excluded: chain N residue 1359 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 143 GLN Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 445 TYR Chi-restraints excluded: chain M residue 498 LEU Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 542 ASN Chi-restraints excluded: chain M residue 546 LEU Chi-restraints excluded: chain M residue 665 LEU Chi-restraints excluded: chain M residue 676 HIS Chi-restraints excluded: chain M residue 712 LEU Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 759 LYS Chi-restraints excluded: chain M residue 822 GLU Chi-restraints excluded: chain M residue 828 VAL Chi-restraints excluded: chain M residue 857 THR Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 895 ASP Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 938 MET Chi-restraints excluded: chain M residue 958 PHE Chi-restraints excluded: chain M residue 977 VAL Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain M residue 1004 PHE Chi-restraints excluded: chain M residue 1086 LEU Chi-restraints excluded: chain M residue 1120 MET Chi-restraints excluded: chain Z residue 218 LYS Chi-restraints excluded: chain X residue 146 ASN Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 326 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 233 optimal weight: 8.9990 chunk 195 optimal weight: 0.8980 chunk 336 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 37 optimal weight: 0.0060 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 528 ASN N 599 GLN N 801 GLN ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN K 11 GLN L 270 GLN ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 608 ASN ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.179771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.177791 restraints weight = 81667.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.177645 restraints weight = 105715.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.177421 restraints weight = 112945.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.177198 restraints weight = 105869.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.177074 restraints weight = 115552.459| |-----------------------------------------------------------------------------| r_work (final): 0.4868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4744 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.725 35130 Z= 0.547 Angle : 0.876 22.950 47419 Z= 0.435 Chirality : 0.048 0.408 5385 Planarity : 0.006 0.096 6096 Dihedral : 7.165 54.621 4758 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 15.57 % Favored : 84.11 % Rotamer: Outliers : 2.80 % Allowed : 22.38 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.65 % Twisted General : 0.31 % 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: -3.45 (0.12), residues: 4297 helix: -0.51 (0.14), residues: 1353 sheet: -3.43 (0.24), residues: 351 loop : -3.32 (0.11), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 479 TYR 0.027 0.002 TYR I 47 PHE 0.052 0.002 PHE M 33 TRP 0.046 0.002 TRP H 40 HIS 0.007 0.001 HIS N1239 Details of bonding type rmsd covalent geometry : bond 0.01569 (35120) covalent geometry : angle 0.87496 (47399) SS BOND : bond 0.00622 ( 10) SS BOND : angle 2.47540 ( 20) hydrogen bonds : bond 0.03546 ( 962) hydrogen bonds : angle 5.25802 ( 2712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 341 time to evaluate : 1.177 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: N 281 MET cc_start: 0.2369 (mmm) cc_final: 0.2125 (mmp) REVERT: N 731 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6426 (tt) REVERT: N 1311 MET cc_start: -0.0071 (pmm) cc_final: -0.1384 (mtt) REVERT: N 1317 MET cc_start: 0.3150 (tmm) cc_final: 0.2360 (tpt) REVERT: B 48 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7548 (mtm) REVERT: B 52 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.6971 (t-90) REVERT: F 133 GLN cc_start: 0.5578 (OUTLIER) cc_final: 0.4999 (mm-40) REVERT: H 202 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7871 (mp) REVERT: H 330 MET cc_start: 0.7660 (mmm) cc_final: 0.7011 (mtp) REVERT: K 114 TYR cc_start: 0.3936 (OUTLIER) cc_final: 0.3679 (m-80) REVERT: M 168 TYR cc_start: 0.7677 (p90) cc_final: 0.7334 (p90) REVERT: M 377 PHE cc_start: 0.4258 (m-10) cc_final: 0.3155 (m-80) REVERT: M 546 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5978 (tt) REVERT: M 676 HIS cc_start: 0.6244 (OUTLIER) cc_final: 0.5935 (m-70) REVERT: M 746 TYR cc_start: 0.5530 (OUTLIER) cc_final: 0.4373 (m-10) REVERT: M 979 HIS cc_start: 0.6028 (OUTLIER) cc_final: 0.5431 (m90) REVERT: M 1069 MET cc_start: 0.6398 (ppp) cc_final: 0.5978 (ppp) REVERT: Z 232 MET cc_start: -0.2211 (tmm) cc_final: -0.2955 (tpt) REVERT: X 385 MET cc_start: 0.0161 (ttt) cc_final: -0.4226 (mtm) REVERT: X 434 MET cc_start: -0.0546 (ttp) cc_final: -0.0921 (ttp) outliers start: 105 outliers final: 66 residues processed: 424 average time/residue: 0.2027 time to fit residues: 142.2388 Evaluate side-chains 381 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 305 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 428 MET Chi-restraints excluded: chain N residue 483 HIS Chi-restraints excluded: chain N residue 581 VAL Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 758 VAL Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 946 ILE Chi-restraints excluded: chain N residue 1064 THR Chi-restraints excluded: chain N residue 1082 THR Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1280 MET Chi-restraints excluded: chain N residue 1343 VAL Chi-restraints excluded: chain N residue 1359 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 143 GLN Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 284 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 445 TYR Chi-restraints excluded: chain M residue 498 LEU Chi-restraints excluded: chain M residue 504 THR Chi-restraints excluded: chain M residue 546 LEU Chi-restraints excluded: chain M residue 676 HIS Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 857 THR Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 895 ASP Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 938 MET Chi-restraints excluded: chain M residue 977 VAL Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain M residue 1086 LEU Chi-restraints excluded: chain M residue 1120 MET Chi-restraints excluded: chain Z residue 218 LYS Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 112 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 322 optimal weight: 0.9990 chunk 260 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 325 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 374 ASN ** N 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 599 GLN N 674 ASN ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 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 = 0.4878 r_free = 0.4878 target = 0.177503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.172617 restraints weight = 81719.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.171917 restraints weight = 134128.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.171629 restraints weight = 151523.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.171292 restraints weight = 138546.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.171201 restraints weight = 145640.199| |-----------------------------------------------------------------------------| r_work (final): 0.4756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4972 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.725 35130 Z= 0.557 Angle : 0.909 22.998 47419 Z= 0.452 Chirality : 0.049 0.311 5385 Planarity : 0.006 0.097 6096 Dihedral : 7.209 54.103 4758 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.33 % Allowed : 16.31 % Favored : 83.36 % Rotamer: Outliers : 2.48 % Allowed : 22.70 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.34 % 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: -3.46 (0.12), residues: 4297 helix: -0.50 (0.14), residues: 1358 sheet: -3.50 (0.23), residues: 367 loop : -3.32 (0.11), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 800 TYR 0.032 0.002 TYR M 674 PHE 0.037 0.002 PHE M 33 TRP 0.038 0.002 TRP H 40 HIS 0.011 0.001 HIS J 78 Details of bonding type rmsd covalent geometry : bond 0.01588 (35120) covalent geometry : angle 0.90801 (47399) SS BOND : bond 0.00610 ( 10) SS BOND : angle 2.42670 ( 20) hydrogen bonds : bond 0.03673 ( 962) hydrogen bonds : angle 5.30226 ( 2712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 319 time to evaluate : 1.389 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: N 281 MET cc_start: 0.2376 (mmm) cc_final: 0.2137 (mmp) REVERT: N 1311 MET cc_start: -0.0135 (pmm) cc_final: -0.1470 (mtt) REVERT: N 1317 MET cc_start: 0.3198 (tmm) cc_final: 0.2344 (tpt) REVERT: B 48 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7510 (mtm) REVERT: B 52 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7118 (t-90) REVERT: F 133 GLN cc_start: 0.5765 (OUTLIER) cc_final: 0.4760 (mm-40) REVERT: H 10 MET cc_start: 0.6190 (ppp) cc_final: 0.5612 (ppp) REVERT: H 198 LEU cc_start: 0.6307 (tp) cc_final: 0.6030 (tp) REVERT: H 202 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8015 (mp) REVERT: H 285 ARG cc_start: 0.7429 (mtm110) cc_final: 0.7033 (ttp80) REVERT: H 330 MET cc_start: 0.7753 (mmm) cc_final: 0.7081 (mtp) REVERT: K 114 TYR cc_start: 0.3987 (OUTLIER) cc_final: 0.3714 (m-80) REVERT: M 168 TYR cc_start: 0.7754 (p90) cc_final: 0.7437 (p90) REVERT: M 377 PHE cc_start: 0.4360 (m-10) cc_final: 0.3507 (m-80) REVERT: M 496 LEU cc_start: 0.7873 (tt) cc_final: 0.7644 (tp) REVERT: M 546 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.5979 (tt) REVERT: M 676 HIS cc_start: 0.6438 (OUTLIER) cc_final: 0.6006 (m-70) REVERT: M 746 TYR cc_start: 0.5708 (OUTLIER) cc_final: 0.4385 (m-10) REVERT: M 979 HIS cc_start: 0.5937 (OUTLIER) cc_final: 0.5629 (m-70) REVERT: M 1010 GLN cc_start: 0.7324 (mp10) cc_final: 0.6638 (mt0) REVERT: M 1069 MET cc_start: 0.6620 (ppp) cc_final: 0.6173 (ppp) REVERT: Z 232 MET cc_start: -0.2240 (tmm) cc_final: -0.2911 (tpt) REVERT: X 385 MET cc_start: -0.0053 (ttt) cc_final: -0.4007 (mtm) REVERT: X 434 MET cc_start: -0.0590 (ttp) cc_final: -0.0932 (ttp) outliers start: 93 outliers final: 73 residues processed: 392 average time/residue: 0.1939 time to fit residues: 126.4747 Evaluate side-chains 387 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 305 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 384 VAL Chi-restraints excluded: chain N residue 428 MET Chi-restraints excluded: chain N residue 480 VAL Chi-restraints excluded: chain N residue 483 HIS Chi-restraints excluded: chain N residue 560 ASP Chi-restraints excluded: chain N residue 567 ILE Chi-restraints excluded: chain N residue 581 VAL Chi-restraints excluded: chain N residue 696 PHE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 758 VAL Chi-restraints excluded: chain N residue 924 VAL Chi-restraints excluded: chain N residue 946 ILE Chi-restraints excluded: chain N residue 1064 THR Chi-restraints excluded: chain N residue 1082 THR Chi-restraints excluded: chain N residue 1176 THR Chi-restraints excluded: chain N residue 1280 MET Chi-restraints excluded: chain N residue 1343 VAL Chi-restraints excluded: chain N residue 1359 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 143 GLN Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 114 TYR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 204 THR Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 276 GLN Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 406 MET Chi-restraints excluded: chain M residue 445 TYR Chi-restraints excluded: chain M residue 498 LEU Chi-restraints excluded: chain M residue 546 LEU Chi-restraints excluded: chain M residue 676 HIS Chi-restraints excluded: chain M residue 746 TYR Chi-restraints excluded: chain M residue 807 GLU Chi-restraints excluded: chain M residue 828 VAL Chi-restraints excluded: chain M residue 864 SER Chi-restraints excluded: chain M residue 895 ASP Chi-restraints excluded: chain M residue 911 VAL Chi-restraints excluded: chain M residue 936 SER Chi-restraints excluded: chain M residue 938 MET Chi-restraints excluded: chain M residue 977 VAL Chi-restraints excluded: chain M residue 979 HIS Chi-restraints excluded: chain M residue 994 THR Chi-restraints excluded: chain M residue 1086 LEU Chi-restraints excluded: chain M residue 1120 MET Chi-restraints excluded: chain Z residue 218 LYS Chi-restraints excluded: chain X residue 354 VAL Chi-restraints excluded: chain X residue 437 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 431 optimal weight: 50.0000 chunk 286 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 178 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 227 optimal weight: 0.0060 chunk 4 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 234 optimal weight: 20.0000 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 599 GLN ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 107 GLN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 608 ASN ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.178488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.175981 restraints weight = 81018.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.175477 restraints weight = 137532.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.175162 restraints weight = 158349.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.175012 restraints weight = 163918.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.174994 restraints weight = 148015.670| |-----------------------------------------------------------------------------| r_work (final): 0.4843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4820 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.725 35130 Z= 0.551 Angle : 0.889 22.849 47419 Z= 0.441 Chirality : 0.048 0.295 5385 Planarity : 0.006 0.087 6096 Dihedral : 7.106 54.490 4758 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.78 % Favored : 83.97 % Rotamer: Outliers : 2.54 % Allowed : 23.13 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.29 % 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: -3.42 (0.12), residues: 4297 helix: -0.45 (0.14), residues: 1359 sheet: -3.56 (0.23), residues: 360 loop : -3.29 (0.11), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 93 TYR 0.026 0.002 TYR I 47 PHE 0.037 0.002 PHE M 33 TRP 0.027 0.002 TRP M 297 HIS 0.008 0.001 HIS N1239 Details of bonding type rmsd covalent geometry : bond 0.01576 (35120) covalent geometry : angle 0.88741 (47399) SS BOND : bond 0.00590 ( 10) SS BOND : angle 2.32318 ( 20) hydrogen bonds : bond 0.03553 ( 962) hydrogen bonds : angle 5.25446 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4551.04 seconds wall clock time: 80 minutes 57.93 seconds (4857.93 seconds total)