Starting phenix.real_space_refine on Fri Aug 7 20:24:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rn2_54078/08_2026/9rn2_54078.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rn2_54078/08_2026/9rn2_54078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rn2_54078/08_2026/9rn2_54078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rn2_54078/08_2026/9rn2_54078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rn2_54078/08_2026/9rn2_54078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rn2_54078/08_2026/9rn2_54078.map" } resolution = 4.1 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= 0.139 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: 5 Type Number sf(0) Gaussians P 276 5.49 5 S 14 5.16 5 C 13490 2.51 5 N 4523 2.21 5 O 5050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23353 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 2352 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 413} Link IDs: {'PTRANS': 11, 'TRANS': 457} Chain breaks: 10 Unresolved non-hydrogen bonds: 1626 Unresolved non-hydrogen angles: 2064 Unresolved non-hydrogen dihedrals: 1368 Unresolved non-hydrogen chiralities: 140 Planarities with less than four sites: {'ARG:plan': 39, 'GLU:plan': 26, 'ASN:plan1': 20, 'PHE:plan': 20, 'GLN:plan1': 28, 'ASP:plan': 19, 'TYR:plan': 19, 'HIS:plan': 17, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 929 Chain: "J" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 1677 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 272} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain breaks: 4 Unresolved non-hydrogen bonds: 980 Unresolved non-hydrogen angles: 1263 Unresolved non-hydrogen dihedrals: 814 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'PHE:plan': 15, 'ASP:plan': 18, 'TYR:plan': 12, 'ARG:plan': 15, 'GLU:plan': 18, 'ASN:plan1': 14, 'TRP:plan': 5, 'GLN:plan1': 15, 'HIS:plan': 8} Unresolved non-hydrogen planarities: 562 Chain: "K" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 1600 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 253} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain breaks: 3 Unresolved non-hydrogen bonds: 922 Unresolved non-hydrogen angles: 1182 Unresolved non-hydrogen dihedrals: 767 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'ASP:plan': 21, 'ASN:plan1': 8, 'PHE:plan': 12, 'ARG:plan': 14, 'TRP:plan': 4, 'GLU:plan': 23, 'HIS:plan': 7, 'TYR:plan': 13, 'GLN:plan1': 9} Unresolved non-hydrogen planarities: 519 Chain: "L" Number of atoms: 1991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 1991 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 338} Link IDs: {'PTRANS': 16, 'TRANS': 379} Chain breaks: 5 Unresolved non-hydrogen bonds: 1157 Unresolved non-hydrogen angles: 1482 Unresolved non-hydrogen dihedrals: 934 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'ASP:plan': 27, 'GLU:plan': 23, 'TRP:plan': 6, 'ARG:plan': 19, 'ASN:plan1': 15, 'TYR:plan': 6, 'PHE:plan': 15, 'GLN:plan1': 16, 'HIS:plan': 6} Unresolved non-hydrogen planarities: 593 Chain: "M" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 1488 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 252} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 920 Unresolved non-hydrogen angles: 1174 Unresolved non-hydrogen dihedrals: 755 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'PHE:plan': 11, 'GLN:plan1': 13, 'GLU:plan': 27, 'ASP:plan': 21, 'TYR:plan': 8, 'ASN:plan1': 12, 'ARG:plan': 18, 'TRP:plan': 5, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 536 Chain: "N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 510 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 8, 'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 7, 'TRP:plan': 2, 'PHE:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 232 Chain: "O" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 895 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 13, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 485 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'HIS:plan': 7, 'TYR:plan': 9, 'TRP:plan': 4, 'PHE:plan': 7, 'ASP:plan': 9, 'ASN:plan1': 8, 'GLU:plan': 14, 'ARG:plan': 11, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 362 Chain: "P" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 189 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 5, 'PHE:plan': 3, 'TYR:plan': 3, 'GLN:plan1': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 351 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 3, 'TRANS': 66} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 5, 'TYR:plan': 6, 'ASP:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 8, 'PHE:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 167 Chain: "V" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 275 Classifications: {'peptide': 68} Incomplete info: {'backbone_only': 63} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'PHE:plan': 5, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "W" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 373 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 5, 'TRANS': 67} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 7, 'HIS:plan': 3, 'ASP:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 160 Chain: "X" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2803 Classifications: {'DNA': 138} Link IDs: {'rna3p': 137} Chain: "Y" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2855 Classifications: {'DNA': 138} Link IDs: {'rna3p': 137} Time building chain proxies: 5.39, per 1000 atoms: 0.23 Number of scatterers: 23353 At special positions: 0 Unit cell: (174.07, 172.38, 194.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 276 15.00 O 5050 8.00 N 4523 7.00 C 13490 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5730 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 27 sheets defined 63.1% alpha, 6.3% beta 137 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.757A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.560A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.435A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.522A pdb=" N LYS D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.924A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.264A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 409 through 429 Processing helix chain 'I' and resid 468 through 509 Processing helix chain 'I' and resid 757 through 770 Processing helix chain 'I' and resid 784 through 798 removed outlier: 3.650A pdb=" N THR I 789 " --> pdb=" O LYS I 785 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE I 790 " --> pdb=" O THR I 786 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU I 792 " --> pdb=" O GLN I 788 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU I 798 " --> pdb=" O THR I 794 " (cutoff:3.500A) Processing helix chain 'I' and resid 812 through 826 removed outlier: 3.602A pdb=" N ASN I 817 " --> pdb=" O SER I 813 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TRP I 818 " --> pdb=" O THR I 814 " (cutoff:3.500A) Processing helix chain 'I' and resid 838 through 844 Processing helix chain 'I' and resid 846 through 850 removed outlier: 3.558A pdb=" N ARG I 849 " --> pdb=" O PRO I 846 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER I 850 " --> pdb=" O GLN I 847 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 846 through 850' Processing helix chain 'I' and resid 862 through 866 Processing helix chain 'I' and resid 891 through 900 removed outlier: 3.811A pdb=" N GLN I 895 " --> pdb=" O CYS I 891 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN I 898 " --> pdb=" O THR I 894 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR I 899 " --> pdb=" O GLN I 895 " (cutoff:3.500A) Processing helix chain 'I' and resid 917 through 925 Processing helix chain 'I' and resid 926 through 928 No H-bonds generated for 'chain 'I' and resid 926 through 928' Processing helix chain 'I' and resid 931 through 939 removed outlier: 3.566A pdb=" N SER I 935 " --> pdb=" O THR I 931 " (cutoff:3.500A) Processing helix chain 'I' and resid 972 through 976 Processing helix chain 'I' and resid 1001 through 1014 Processing helix chain 'I' and resid 1039 through 1048 Processing helix chain 'I' and resid 1049 through 1051 No H-bonds generated for 'chain 'I' and resid 1049 through 1051' Processing helix chain 'I' and resid 1052 through 1059 Processing helix chain 'I' and resid 1075 through 1079 removed outlier: 4.118A pdb=" N SER I1079 " --> pdb=" O LEU I1075 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1075 through 1079' Processing helix chain 'I' and resid 1079 through 1095 removed outlier: 3.578A pdb=" N ARG I1087 " --> pdb=" O GLU I1083 " (cutoff:3.500A) Proline residue: I1090 - end of helix Processing helix chain 'I' and resid 1107 through 1120 removed outlier: 4.228A pdb=" N ILE I1111 " --> pdb=" O SER I1107 " (cutoff:3.500A) Processing helix chain 'I' and resid 1179 through 1188 removed outlier: 4.123A pdb=" N ASP I1183 " --> pdb=" O ASN I1179 " (cutoff:3.500A) Processing helix chain 'I' and resid 1309 through 1325 removed outlier: 4.410A pdb=" N PHE I1313 " --> pdb=" O HIS I1309 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP I1314 " --> pdb=" O GLU I1310 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG I1318 " --> pdb=" O ASP I1314 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET I1319 " --> pdb=" O LEU I1315 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP I1320 " --> pdb=" O PHE I1316 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU I1321 " --> pdb=" O MET I1317 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 77 Processing helix chain 'J' and resid 95 through 109 Processing helix chain 'J' and resid 129 through 143 Processing helix chain 'J' and resid 154 through 162 Processing helix chain 'J' and resid 189 through 192 Processing helix chain 'J' and resid 198 through 214 Processing helix chain 'J' and resid 247 through 267 removed outlier: 3.510A pdb=" N HIS J 251 " --> pdb=" O THR J 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 299 through 307 Proline residue: J 305 - end of helix Processing helix chain 'J' and resid 308 through 310 No H-bonds generated for 'chain 'J' and resid 308 through 310' Processing helix chain 'J' and resid 324 through 335 Processing helix chain 'J' and resid 340 through 346 Processing helix chain 'J' and resid 352 through 357 removed outlier: 3.739A pdb=" N THR J 355 " --> pdb=" O GLY J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 372 Processing helix chain 'J' and resid 381 through 390 removed outlier: 5.886A pdb=" N VAL J 387 " --> pdb=" O ASN J 384 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU J 388 " --> pdb=" O THR J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 401 Processing helix chain 'J' and resid 403 through 409 Processing helix chain 'K' and resid 3 through 7 Processing helix chain 'K' and resid 80 through 91 removed outlier: 4.301A pdb=" N TYR K 91 " --> pdb=" O HIS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 124 removed outlier: 4.168A pdb=" N ARG K 116 " --> pdb=" O PRO K 112 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR K 120 " --> pdb=" O ARG K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 145 Processing helix chain 'K' and resid 171 through 175 Processing helix chain 'K' and resid 181 through 197 Processing helix chain 'K' and resid 202 through 216 removed outlier: 3.836A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL K 209 " --> pdb=" O GLU K 205 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG K 210 " --> pdb=" O ARG K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 232 Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 258 through 262 Processing helix chain 'K' and resid 263 through 268 removed outlier: 3.704A pdb=" N LEU K 267 " --> pdb=" O GLN K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 285 Processing helix chain 'K' and resid 288 through 295 removed outlier: 4.384A pdb=" N ASP K 292 " --> pdb=" O ASP K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 306 removed outlier: 3.729A pdb=" N TYR K 306 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 347 Processing helix chain 'K' and resid 349 through 354 removed outlier: 3.667A pdb=" N GLN K 354 " --> pdb=" O SER K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 366 removed outlier: 3.591A pdb=" N GLU K 364 " --> pdb=" O GLN K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 372 Processing helix chain 'L' and resid 1660 through 1665 removed outlier: 3.640A pdb=" N ILE L1664 " --> pdb=" O THR L1660 " (cutoff:3.500A) Processing helix chain 'L' and resid 1668 through 1678 Processing helix chain 'L' and resid 1680 through 1697 Processing helix chain 'L' and resid 1700 through 1704 Processing helix chain 'L' and resid 1711 through 1729 Processing helix chain 'L' and resid 1731 through 1735 removed outlier: 3.900A pdb=" N GLU L1735 " --> pdb=" O LYS L1732 " (cutoff:3.500A) Processing helix chain 'L' and resid 1740 through 1744 Processing helix chain 'L' and resid 1840 through 1846 Processing helix chain 'L' and resid 1973 through 1992 Processing helix chain 'L' and resid 1996 through 2003 removed outlier: 4.380A pdb=" N GLU L2000 " --> pdb=" O GLY L1996 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS L2003 " --> pdb=" O PHE L1999 " (cutoff:3.500A) Processing helix chain 'L' and resid 2004 through 2016 removed outlier: 4.278A pdb=" N LEU L2016 " --> pdb=" O GLY L2012 " (cutoff:3.500A) Processing helix chain 'L' and resid 2051 through 2068 Processing helix chain 'L' and resid 2077 through 2093 Proline residue: L2083 - end of helix Processing helix chain 'L' and resid 2115 through 2126 Processing helix chain 'L' and resid 2128 through 2137 Processing helix chain 'L' and resid 2140 through 2158 removed outlier: 4.393A pdb=" N ARG L2158 " --> pdb=" O PHE L2154 " (cutoff:3.500A) Processing helix chain 'L' and resid 2160 through 2178 Processing helix chain 'L' and resid 2178 through 2187 Processing helix chain 'L' and resid 2190 through 2210 Processing helix chain 'L' and resid 2227 through 2243 Processing helix chain 'L' and resid 2244 through 2249 removed outlier: 4.641A pdb=" N ASN L2247 " --> pdb=" O VAL L2244 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER L2249 " --> pdb=" O GLU L2246 " (cutoff:3.500A) Processing helix chain 'L' and resid 2254 through 2264 Processing helix chain 'L' and resid 2268 through 2284 removed outlier: 3.692A pdb=" N VAL L2274 " --> pdb=" O LEU L2270 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 36 Processing helix chain 'M' and resid 41 through 47 removed outlier: 3.526A pdb=" N LYS M 45 " --> pdb=" O GLY M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 66 Processing helix chain 'M' and resid 79 through 84 Processing helix chain 'M' and resid 93 through 100 removed outlier: 3.736A pdb=" N LEU M 100 " --> pdb=" O VAL M 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 Processing helix chain 'M' and resid 214 through 226 Processing helix chain 'M' and resid 229 through 247 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 289 through 302 Processing helix chain 'M' and resid 304 through 326 Processing helix chain 'M' and resid 342 through 350 removed outlier: 4.200A pdb=" N GLN M 348 " --> pdb=" O GLY M 344 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS M 350 " --> pdb=" O ALA M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 357 through 381 Processing helix chain 'N' and resid 427 through 433 removed outlier: 4.314A pdb=" N TRP N 432 " --> pdb=" O TYR N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 440 through 446 Processing helix chain 'N' and resid 447 through 450 Processing helix chain 'N' and resid 458 through 475 Processing helix chain 'N' and resid 482 through 490 Processing helix chain 'N' and resid 493 through 507 Processing helix chain 'O' and resid 439 through 446 Processing helix chain 'O' and resid 447 through 450 Processing helix chain 'O' and resid 458 through 474 Processing helix chain 'O' and resid 482 through 490 Processing helix chain 'O' and resid 493 through 507 Processing helix chain 'O' and resid 602 through 614 Processing helix chain 'O' and resid 619 through 628 Processing helix chain 'O' and resid 631 through 641 Processing helix chain 'P' and resid 474 through 478 removed outlier: 3.896A pdb=" N ARG P 478 " --> pdb=" O GLU P 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 474 through 478' Processing helix chain 'P' and resid 479 through 485 removed outlier: 3.858A pdb=" N GLN P 484 " --> pdb=" O PHE P 481 " (cutoff:3.500A) Proline residue: P 485 - end of helix Processing helix chain 'P' and resid 486 through 509 Processing helix chain 'R' and resid 14 through 39 Processing helix chain 'R' and resid 58 through 62 Processing helix chain 'V' and resid 142 through 160 Processing helix chain 'V' and resid 163 through 176 removed outlier: 3.637A pdb=" N GLY V 168 " --> pdb=" O GLN V 164 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY V 172 " --> pdb=" O GLY V 168 " (cutoff:3.500A) Processing helix chain 'V' and resid 180 through 190 Processing helix chain 'V' and resid 193 through 206 Proline residue: V 202 - end of helix Processing helix chain 'W' and resid 46 through 61 removed outlier: 3.578A pdb=" N GLY W 54 " --> pdb=" O VAL W 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 82 Processing helix chain 'W' and resid 83 through 105 Proline residue: W 89 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.967A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.262A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.746A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.908A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.025A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'I' and resid 992 through 998 removed outlier: 6.559A pdb=" N VAL I 992 " --> pdb=" O VAL I1201 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ARG I1203 " --> pdb=" O VAL I 992 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR I 994 " --> pdb=" O ARG I1203 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N CYS I1205 " --> pdb=" O TYR I 994 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE I 996 " --> pdb=" O CYS I1205 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL I1099 " --> pdb=" O PHE I1152 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU I1154 " --> pdb=" O VAL I1099 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU I1101 " --> pdb=" O LEU I1154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 35 through 37 removed outlier: 6.675A pdb=" N LEU J 14 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N SER J 123 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N PHE J 16 " --> pdb=" O SER J 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AB5, first strand: chain 'J' and resid 88 through 89 Processing sheet with id=AB6, first strand: chain 'J' and resid 186 through 187 Processing sheet with id=AB7, first strand: chain 'J' and resid 186 through 187 Processing sheet with id=AB8, first strand: chain 'J' and resid 280 through 281 Processing sheet with id=AB9, first strand: chain 'K' and resid 18 through 21 removed outlier: 6.699A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 176 through 178 removed outlier: 6.072A pdb=" N ILE K 151 " --> pdb=" O VAL K 298 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N SER K 300 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N MET K 153 " --> pdb=" O SER K 300 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 239 through 241 Processing sheet with id=AC3, first strand: chain 'L' and resid 1814 through 1816 Processing sheet with id=AC4, first strand: chain 'M' and resid 17 through 18 Processing sheet with id=AC5, first strand: chain 'M' and resid 186 through 195 Processing sheet with id=AC6, first strand: chain 'M' and resid 261 through 270 Processing sheet with id=AC7, first strand: chain 'N' and resid 424 through 426 removed outlier: 6.431A pdb=" N ILE N 424 " --> pdb=" O LEU O 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'N' and resid 437 through 439 removed outlier: 3.718A pdb=" N TYR R 72 " --> pdb=" O VAL N 438 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 523 through 524 1384 hydrogen bonds defined for protein. 3927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 702 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 7.89 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4539 1.33 - 1.45: 6136 1.45 - 1.57: 12992 1.57 - 1.69: 492 1.69 - 1.81: 24 Bond restraints: 24183 Sorted by residual: bond pdb=" C3' DA Y 91 " pdb=" O3' DA Y 91 " ideal model delta sigma weight residual 1.435 1.327 0.108 1.30e-02 5.92e+03 6.84e+01 bond pdb=" C5' DT Y 13 " pdb=" C4' DT Y 13 " ideal model delta sigma weight residual 1.512 1.559 -0.047 7.00e-03 2.04e+04 4.53e+01 bond pdb=" C3' DG Y 31 " pdb=" O3' DG Y 31 " ideal model delta sigma weight residual 1.435 1.349 0.086 1.30e-02 5.92e+03 4.37e+01 bond pdb=" C5' DT Y 14 " pdb=" C4' DT Y 14 " ideal model delta sigma weight residual 1.512 1.558 -0.046 7.00e-03 2.04e+04 4.23e+01 bond pdb=" C3' DC X 80 " pdb=" O3' DC X 80 " ideal model delta sigma weight residual 1.435 1.358 0.077 1.30e-02 5.92e+03 3.50e+01 ... (remaining 24178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 31614 2.07 - 4.14: 2123 4.14 - 6.20: 463 6.20 - 8.27: 130 8.27 - 10.34: 7 Bond angle restraints: 34337 Sorted by residual: angle pdb=" O5' DT X 129 " pdb=" C5' DT X 129 " pdb=" C4' DT X 129 " ideal model delta sigma weight residual 109.40 119.69 -10.29 8.00e-01 1.56e+00 1.65e+02 angle pdb=" O5' DC X 134 " pdb=" C5' DC X 134 " pdb=" C4' DC X 134 " ideal model delta sigma weight residual 109.40 116.08 -6.68 8.00e-01 1.56e+00 6.96e+01 angle pdb=" O5' DT Y 13 " pdb=" C5' DT Y 13 " pdb=" C4' DT Y 13 " ideal model delta sigma weight residual 109.40 115.75 -6.35 8.00e-01 1.56e+00 6.31e+01 angle pdb=" O5' DG Y 15 " pdb=" C5' DG Y 15 " pdb=" C4' DG Y 15 " ideal model delta sigma weight residual 109.40 115.23 -5.83 8.00e-01 1.56e+00 5.31e+01 angle pdb=" O5' DT Y 14 " pdb=" C5' DT Y 14 " pdb=" C4' DT Y 14 " ideal model delta sigma weight residual 109.40 115.16 -5.76 8.00e-01 1.56e+00 5.18e+01 ... (remaining 34332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 11589 16.96 - 33.92: 652 33.92 - 50.88: 1035 50.88 - 67.85: 401 67.85 - 84.81: 4 Dihedral angle restraints: 13681 sinusoidal: 4873 harmonic: 8808 Sorted by residual: dihedral pdb=" CA ARG C 36 " pdb=" C ARG C 36 " pdb=" N LYS C 37 " pdb=" CA LYS C 37 " ideal model delta harmonic sigma weight residual 180.00 153.29 26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA ASN I 926 " pdb=" C ASN I 926 " pdb=" N PHE I 927 " pdb=" CA PHE I 927 " ideal model delta harmonic sigma weight residual -180.00 -153.72 -26.28 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA HIS I 868 " pdb=" C HIS I 868 " pdb=" N ILE I 869 " pdb=" CA ILE I 869 " ideal model delta harmonic sigma weight residual -180.00 -155.52 -24.48 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 13678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3281 0.085 - 0.169: 686 0.169 - 0.254: 215 0.254 - 0.338: 20 0.338 - 0.423: 2 Chirality restraints: 4204 Sorted by residual: chirality pdb=" CA ASP L1663 " pdb=" N ASP L1663 " pdb=" C ASP L1663 " pdb=" CB ASP L1663 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C3' DT X 125 " pdb=" C4' DT X 125 " pdb=" O3' DT X 125 " pdb=" C2' DT X 125 " both_signs ideal model delta sigma weight residual False -2.73 -2.36 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C3' DA Y 19 " pdb=" C4' DA Y 19 " pdb=" O3' DA Y 19 " pdb=" C2' DA Y 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 4201 not shown) Planarity restraints: 3714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA X 120 " -0.066 2.00e-02 2.50e+03 2.82e-02 2.19e+01 pdb=" N9 DA X 120 " 0.053 2.00e-02 2.50e+03 pdb=" C8 DA X 120 " 0.014 2.00e-02 2.50e+03 pdb=" N7 DA X 120 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DA X 120 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA X 120 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA X 120 " -0.034 2.00e-02 2.50e+03 pdb=" N1 DA X 120 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA X 120 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DA X 120 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DA X 120 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA X 39 " -0.065 2.00e-02 2.50e+03 2.76e-02 2.10e+01 pdb=" N9 DA X 39 " 0.051 2.00e-02 2.50e+03 pdb=" C8 DA X 39 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DA X 39 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DA X 39 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA X 39 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA X 39 " -0.033 2.00e-02 2.50e+03 pdb=" N1 DA X 39 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA X 39 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA X 39 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DA X 39 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA X 69 " -0.065 2.00e-02 2.50e+03 2.76e-02 2.09e+01 pdb=" N9 DA X 69 " 0.052 2.00e-02 2.50e+03 pdb=" C8 DA X 69 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DA X 69 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DA X 69 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA X 69 " 0.000 2.00e-02 2.50e+03 pdb=" N6 DA X 69 " -0.031 2.00e-02 2.50e+03 pdb=" N1 DA X 69 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA X 69 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DA X 69 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DA X 69 " 0.010 2.00e-02 2.50e+03 ... (remaining 3711 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2523 2.75 - 3.29: 23100 3.29 - 3.83: 39841 3.83 - 4.36: 44425 4.36 - 4.90: 66571 Nonbonded interactions: 176460 Sorted by model distance: nonbonded pdb=" OG1 THR C 17 " pdb=" OG SER C 20 " model vdw 2.213 3.040 nonbonded pdb=" O THR I 859 " pdb=" N ILE I 863 " model vdw 2.379 3.120 nonbonded pdb=" O LEU C 34 " pdb=" O LYS C 37 " model vdw 2.438 3.040 nonbonded pdb=" O GLU N 414 " pdb=" O ARG R 78 " model vdw 2.448 3.040 nonbonded pdb=" OG1 THR D 91 " pdb=" OE1 GLU D 94 " model vdw 2.465 3.040 ... (remaining 176455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 125) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 27.610 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4377 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 : 0.009 0.108 24183 Z= 0.809 Angle : 1.221 10.339 34337 Z= 0.798 Chirality : 0.079 0.423 4204 Planarity : 0.008 0.111 3714 Dihedral : 22.427 84.806 7951 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.10 % Favored : 96.77 % Rotamer: Outliers : 0.28 % Allowed : 1.10 % Favored : 98.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3004 helix: 0.21 (0.11), residues: 1767 sheet: -0.20 (0.40), residues: 157 loop : -0.35 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 64 TYR 0.049 0.004 TYR H 122 PHE 0.050 0.003 PHE E 85 TRP 0.000 0.000 TRP I 764 HIS 0.015 0.003 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00943 / 0.81 (24183) covalent geometry : angle 1.22088 / 0.80 (34337) hydrogen bonds : bond 0.14747 / 9.95 ( 1733) hydrogen bonds : angle 5.77078 / 4.16 ( 4629) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.836 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: A 61 LEU cc_start: 0.9181 (mt) cc_final: 0.8707 (pp) REVERT: A 71 LEU cc_start: 0.9874 (tp) cc_final: 0.9666 (mt) REVERT: A 80 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8489 (tptp) REVERT: A 83 LEU cc_start: 0.8965 (mt) cc_final: 0.8681 (mt) REVERT: A 104 LEU cc_start: 0.9747 (tp) cc_final: 0.9491 (mt) REVERT: A 105 PHE cc_start: 0.9749 (m-80) cc_final: 0.9353 (m-80) REVERT: A 107 ASP cc_start: 0.9495 (m-30) cc_final: 0.8996 (m-30) REVERT: A 110 LEU cc_start: 0.9720 (mt) cc_final: 0.9105 (mt) REVERT: A 120 ILE cc_start: 0.9689 (pt) cc_final: 0.9442 (pt) REVERT: B 54 GLU cc_start: 0.9538 (mm-30) cc_final: 0.9251 (mm-30) REVERT: B 64 GLU cc_start: 0.9538 (mt-10) cc_final: 0.9300 (mt-10) REVERT: B 98 LEU cc_start: 0.9596 (tp) cc_final: 0.9353 (tp) REVERT: C 26 PHE cc_start: 0.8850 (m-80) cc_final: 0.8531 (m-10) REVERT: C 57 GLU cc_start: 0.8952 (tt0) cc_final: 0.8516 (tt0) REVERT: C 65 GLU cc_start: 0.9506 (tt0) cc_final: 0.9189 (tp30) REVERT: C 100 ARG cc_start: 0.9110 (mmm160) cc_final: 0.8736 (mmm160) REVERT: C 112 ILE cc_start: 0.5512 (mt) cc_final: 0.4984 (tt) REVERT: D 60 MET cc_start: 0.8959 (tpp) cc_final: 0.8722 (tpp) REVERT: D 63 MET cc_start: 0.9794 (mmm) cc_final: 0.9575 (mmm) REVERT: D 72 GLU cc_start: 0.9321 (tt0) cc_final: 0.9093 (mt-10) REVERT: D 103 LEU cc_start: 0.9549 (mt) cc_final: 0.9099 (tp) REVERT: E 51 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8842 (mt-10) REVERT: E 55 TYR cc_start: 0.9450 (m-80) cc_final: 0.9128 (m-10) REVERT: E 85 PHE cc_start: 0.9449 (m-80) cc_final: 0.9139 (m-80) REVERT: E 105 PHE cc_start: 0.9706 (m-80) cc_final: 0.9376 (m-80) REVERT: E 110 LEU cc_start: 0.9714 (mt) cc_final: 0.9246 (mp) REVERT: F 64 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9372 (mt-10) REVERT: F 69 ASP cc_start: 0.9515 (m-30) cc_final: 0.8812 (t0) REVERT: G 91 ASP cc_start: 0.9351 (t0) cc_final: 0.9066 (t0) REVERT: G 94 LEU cc_start: 0.9837 (mt) cc_final: 0.9408 (mt) REVERT: G 102 THR cc_start: 0.9620 (m) cc_final: 0.9349 (p) REVERT: H 66 PHE cc_start: 0.9668 (t80) cc_final: 0.9380 (t80) REVERT: H 102 LEU cc_start: 0.9545 (mt) cc_final: 0.9232 (mt) REVERT: H 107 LEU cc_start: 0.9691 (mp) cc_final: 0.9486 (mt) outliers start: 2 outliers final: 0 residues processed: 294 average time/residue: 0.1462 time to fit residues: 70.0418 Evaluate side-chains 212 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 5.9990 overall best weight: 8.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN C 39 ASN D 110 HIS E 69 GLN F 94 GLN H 83 HIS H 110 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.121470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.082191 restraints weight = 100782.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.084194 restraints weight = 54705.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.085413 restraints weight = 36137.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.086500 restraints weight = 26973.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.087253 restraints weight = 21564.165| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.173 24183 Z= 0.409 Angle : 0.999 14.538 34337 Z= 0.527 Chirality : 0.053 0.285 4204 Planarity : 0.006 0.067 3714 Dihedral : 26.322 76.514 6163 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.14 % Allowed : 3.58 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 3004 helix: 0.74 (0.12), residues: 1794 sheet: -0.31 (0.43), residues: 160 loop : -0.54 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.046 0.002 ARG D 80 TYR 0.024 0.003 TYR D 43 PHE 0.017 0.002 PHE E 68 TRP 0.000 0.000 TRP I 764 HIS 0.011 0.003 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.41 (24183) covalent geometry : angle 0.99873 / 0.53 (34337) hydrogen bonds : bond 0.11724 / 7.94 ( 1733) hydrogen bonds : angle 5.00730 / 3.61 ( 4629) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9342 (mt-10) cc_final: 0.9004 (mt-10) REVERT: A 91 MET cc_start: 0.9538 (mtm) cc_final: 0.9232 (mtp) REVERT: A 106 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8653 (tm-30) REVERT: B 60 LYS cc_start: 0.9637 (tttt) cc_final: 0.9103 (ptmm) REVERT: B 69 ASP cc_start: 0.9606 (m-30) cc_final: 0.9357 (m-30) REVERT: B 94 GLN cc_start: 0.9140 (tm-30) cc_final: 0.8824 (tm-30) REVERT: C 57 GLU cc_start: 0.9111 (tt0) cc_final: 0.8528 (mt-10) REVERT: C 65 GLU cc_start: 0.9612 (tt0) cc_final: 0.9240 (tm-30) REVERT: D 70 ILE cc_start: 0.9694 (mm) cc_final: 0.9398 (mm) REVERT: E 51 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8508 (mt-10) REVERT: E 55 TYR cc_start: 0.9243 (m-80) cc_final: 0.9038 (m-80) REVERT: E 105 PHE cc_start: 0.9538 (m-80) cc_final: 0.9322 (m-80) REVERT: F 64 GLU cc_start: 0.9552 (mt-10) cc_final: 0.9251 (mt-10) REVERT: F 69 ASP cc_start: 0.9321 (m-30) cc_final: 0.9012 (t0) REVERT: G 91 ASP cc_start: 0.9238 (t0) cc_final: 0.8652 (t0) REVERT: G 94 LEU cc_start: 0.9769 (mt) cc_final: 0.9516 (mt) REVERT: H 66 PHE cc_start: 0.9635 (t80) cc_final: 0.9322 (t80) REVERT: H 114 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9152 (mm-30) outliers start: 1 outliers final: 1 residues processed: 195 average time/residue: 0.1334 time to fit residues: 43.8477 Evaluate side-chains 159 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 168 optimal weight: 9.9990 chunk 293 optimal weight: 30.0000 chunk 252 optimal weight: 50.0000 chunk 260 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 220 optimal weight: 50.0000 chunk 180 optimal weight: 0.0770 chunk 143 optimal weight: 0.0170 chunk 41 optimal weight: 7.9990 chunk 162 optimal weight: 50.0000 overall best weight: 2.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.128004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.086248 restraints weight = 97767.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.088507 restraints weight = 50249.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.089975 restraints weight = 32025.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.090931 restraints weight = 23238.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.091720 restraints weight = 18704.311| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24183 Z= 0.153 Angle : 0.646 9.134 34337 Z= 0.355 Chirality : 0.043 0.216 4204 Planarity : 0.004 0.050 3714 Dihedral : 25.803 87.034 6163 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.28 % Allowed : 2.89 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.15), residues: 3004 helix: 1.71 (0.12), residues: 1805 sheet: -0.22 (0.43), residues: 160 loop : -0.36 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 117 TYR 0.015 0.001 TYR F 52 PHE 0.023 0.001 PHE D 71 TRP 0.000 0.000 TRP I 764 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (24183) covalent geometry : angle 0.64564 / 0.36 (34337) hydrogen bonds : bond 0.04821 / 3.19 ( 1733) hydrogen bonds : angle 3.95859 / 2.86 ( 4629) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 215 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.9507 (mtm) cc_final: 0.9245 (mtp) REVERT: A 105 PHE cc_start: 0.9594 (m-80) cc_final: 0.9126 (m-10) REVERT: A 121 MET cc_start: 0.8766 (ptp) cc_final: 0.8517 (ptp) REVERT: B 60 LYS cc_start: 0.9506 (tttt) cc_final: 0.9196 (ptpp) REVERT: B 68 ARG cc_start: 0.9429 (ttp-110) cc_final: 0.9010 (ttm110) REVERT: B 69 ASP cc_start: 0.9423 (m-30) cc_final: 0.9139 (m-30) REVERT: B 94 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8861 (tm-30) REVERT: C 57 GLU cc_start: 0.9132 (tt0) cc_final: 0.8539 (tt0) REVERT: C 65 GLU cc_start: 0.9584 (tt0) cc_final: 0.9158 (tm-30) REVERT: D 63 MET cc_start: 0.9569 (mmp) cc_final: 0.9335 (mmm) REVERT: D 90 ILE cc_start: 0.9606 (tp) cc_final: 0.9353 (tp) REVERT: E 51 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8310 (mt-10) REVERT: E 55 TYR cc_start: 0.9321 (m-80) cc_final: 0.8967 (m-80) REVERT: E 91 MET cc_start: 0.9488 (mmp) cc_final: 0.9222 (mmm) REVERT: E 95 GLU cc_start: 0.8755 (tp30) cc_final: 0.8494 (tp30) REVERT: E 104 LEU cc_start: 0.9513 (mm) cc_final: 0.9239 (mm) REVERT: E 105 PHE cc_start: 0.9481 (m-80) cc_final: 0.9151 (m-10) REVERT: E 106 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8544 (tm-30) REVERT: F 61 VAL cc_start: 0.9881 (t) cc_final: 0.9397 (t) REVERT: F 64 GLU cc_start: 0.9454 (mt-10) cc_final: 0.9020 (mt-10) REVERT: F 69 ASP cc_start: 0.9152 (m-30) cc_final: 0.8725 (m-30) REVERT: F 94 GLN cc_start: 0.8470 (mp10) cc_final: 0.8235 (mp10) REVERT: G 91 ASP cc_start: 0.9070 (t0) cc_final: 0.8562 (t0) REVERT: H 66 PHE cc_start: 0.9490 (t80) cc_final: 0.9126 (t80) REVERT: H 101 LEU cc_start: 0.9793 (mt) cc_final: 0.9588 (mt) REVERT: H 107 LEU cc_start: 0.9685 (mt) cc_final: 0.9460 (mt) REVERT: H 114 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9107 (mm-30) outliers start: 2 outliers final: 0 residues processed: 215 average time/residue: 0.1317 time to fit residues: 47.9314 Evaluate side-chains 175 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 244 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 40.0000 chunk 186 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 chunk 316 optimal weight: 40.0000 chunk 168 optimal weight: 30.0000 chunk 320 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 293 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.155165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.108219 restraints weight = 194942.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.107778 restraints weight = 86716.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.108055 restraints weight = 51019.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.108496 restraints weight = 42540.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.108397 restraints weight = 36327.349| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 24183 Z= 0.218 Angle : 0.686 11.572 34337 Z= 0.376 Chirality : 0.043 0.229 4204 Planarity : 0.004 0.046 3714 Dihedral : 25.487 82.784 6163 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.15), residues: 3004 helix: 1.76 (0.12), residues: 1800 sheet: -0.15 (0.42), residues: 168 loop : -0.36 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 73 TYR 0.023 0.002 TYR B 89 PHE 0.017 0.001 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.008 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.22 (24183) covalent geometry : angle 0.68551 / 0.38 (34337) hydrogen bonds : bond 0.07061 / 4.70 ( 1733) hydrogen bonds : angle 3.96100 / 2.87 ( 4629) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.9523 (mtm) cc_final: 0.9253 (mtp) REVERT: A 121 MET cc_start: 0.8364 (ptp) cc_final: 0.7725 (ptp) REVERT: A 130 ARG cc_start: 0.8807 (mmp80) cc_final: 0.8525 (mmp80) REVERT: B 60 LYS cc_start: 0.9401 (tttt) cc_final: 0.9030 (ptmm) REVERT: B 64 GLU cc_start: 0.9094 (mp0) cc_final: 0.8866 (mp0) REVERT: B 94 GLN cc_start: 0.9239 (tm-30) cc_final: 0.8918 (tm-30) REVERT: C 57 GLU cc_start: 0.9080 (tt0) cc_final: 0.8372 (tt0) REVERT: C 65 GLU cc_start: 0.9581 (tt0) cc_final: 0.9048 (tp30) REVERT: C 97 LEU cc_start: 0.9674 (tp) cc_final: 0.9452 (tt) REVERT: D 63 MET cc_start: 0.9665 (mmp) cc_final: 0.9413 (mmm) REVERT: D 90 ILE cc_start: 0.9600 (tp) cc_final: 0.9389 (tp) REVERT: E 51 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8260 (mt-10) REVERT: E 55 TYR cc_start: 0.9335 (m-80) cc_final: 0.8978 (m-80) REVERT: E 91 MET cc_start: 0.9493 (mmp) cc_final: 0.9199 (mmm) REVERT: E 95 GLU cc_start: 0.8816 (tp30) cc_final: 0.8503 (tp30) REVERT: E 101 LEU cc_start: 0.9846 (mm) cc_final: 0.9592 (mm) REVERT: E 104 LEU cc_start: 0.9507 (mm) cc_final: 0.9167 (mm) REVERT: E 105 PHE cc_start: 0.9521 (m-80) cc_final: 0.9175 (m-80) REVERT: E 106 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8407 (tm-30) REVERT: F 64 GLU cc_start: 0.9357 (mt-10) cc_final: 0.8981 (mt-10) REVERT: F 69 ASP cc_start: 0.8954 (m-30) cc_final: 0.8692 (m-30) REVERT: G 88 ILE cc_start: 0.9791 (tp) cc_final: 0.9520 (pt) REVERT: H 66 PHE cc_start: 0.9614 (t80) cc_final: 0.9335 (t80) REVERT: H 114 GLU cc_start: 0.9297 (mm-30) cc_final: 0.9040 (mm-30) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1138 time to fit residues: 36.6202 Evaluate side-chains 161 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 249 optimal weight: 30.0000 chunk 271 optimal weight: 0.2980 chunk 313 optimal weight: 30.0000 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 248 optimal weight: 50.0000 chunk 86 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.156951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.119268 restraints weight = 194718.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.115020 restraints weight = 125550.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.115200 restraints weight = 84111.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.114859 restraints weight = 58031.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.115029 restraints weight = 60622.268| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24183 Z= 0.133 Angle : 0.587 9.426 34337 Z= 0.327 Chirality : 0.041 0.208 4204 Planarity : 0.004 0.063 3714 Dihedral : 25.276 81.847 6163 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.16), residues: 3004 helix: 2.18 (0.12), residues: 1788 sheet: -0.15 (0.42), residues: 171 loop : -0.26 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 53 TYR 0.021 0.001 TYR D 84 PHE 0.017 0.001 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.006 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (24183) covalent geometry : angle 0.58691 / 0.33 (34337) hydrogen bonds : bond 0.03905 / 2.58 ( 1733) hydrogen bonds : angle 3.60049 / 2.60 ( 4629) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9760 (tt0) cc_final: 0.9382 (pt0) REVERT: A 91 MET cc_start: 0.9596 (mtm) cc_final: 0.9215 (mtp) REVERT: A 121 MET cc_start: 0.8839 (ptp) cc_final: 0.8468 (mtp) REVERT: B 64 GLU cc_start: 0.9243 (mp0) cc_final: 0.8879 (mp0) REVERT: B 94 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8925 (tm-30) REVERT: C 57 GLU cc_start: 0.9143 (tt0) cc_final: 0.8616 (tt0) REVERT: C 65 GLU cc_start: 0.9568 (tt0) cc_final: 0.9149 (tm-30) REVERT: C 115 VAL cc_start: 0.7189 (t) cc_final: 0.6668 (t) REVERT: D 63 MET cc_start: 0.9680 (mmp) cc_final: 0.9433 (mmm) REVERT: D 70 ILE cc_start: 0.9610 (mm) cc_final: 0.9400 (mm) REVERT: D 77 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9132 (mm-30) REVERT: D 90 ILE cc_start: 0.9534 (tp) cc_final: 0.9311 (tp) REVERT: D 103 LEU cc_start: 0.9640 (mm) cc_final: 0.9074 (tp) REVERT: E 51 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8309 (mt-10) REVERT: E 55 TYR cc_start: 0.9321 (m-80) cc_final: 0.8907 (m-80) REVERT: E 91 MET cc_start: 0.9513 (mmp) cc_final: 0.9213 (mmm) REVERT: E 95 GLU cc_start: 0.8894 (tp30) cc_final: 0.8532 (tp30) REVERT: E 101 LEU cc_start: 0.9871 (mm) cc_final: 0.9562 (mm) REVERT: E 104 LEU cc_start: 0.9556 (mm) cc_final: 0.9316 (mm) REVERT: E 105 PHE cc_start: 0.9568 (m-80) cc_final: 0.9202 (m-80) REVERT: E 106 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8578 (tm-30) REVERT: F 61 VAL cc_start: 0.9738 (t) cc_final: 0.9128 (t) REVERT: F 64 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8930 (mt-10) REVERT: G 97 LEU cc_start: 0.9543 (mt) cc_final: 0.9307 (mt) REVERT: H 66 PHE cc_start: 0.9647 (t80) cc_final: 0.9370 (t80) REVERT: H 101 LEU cc_start: 0.9688 (mt) cc_final: 0.9459 (mt) REVERT: H 114 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9102 (mm-30) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1247 time to fit residues: 43.8606 Evaluate side-chains 169 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 323 optimal weight: 20.0000 chunk 227 optimal weight: 40.0000 chunk 144 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 124 optimal weight: 50.0000 chunk 169 optimal weight: 50.0000 chunk 196 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 118 optimal weight: 40.0000 overall best weight: 10.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.115507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.077081 restraints weight = 104118.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.078700 restraints weight = 59601.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.080058 restraints weight = 41533.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.080933 restraints weight = 31047.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.081605 restraints weight = 24965.888| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 24183 Z= 0.458 Angle : 0.991 21.222 34337 Z= 0.540 Chirality : 0.053 0.297 4204 Planarity : 0.007 0.085 3714 Dihedral : 25.994 86.921 6163 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 3004 helix: 0.83 (0.12), residues: 1793 sheet: -0.41 (0.43), residues: 152 loop : -0.85 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG E 41 TYR 0.025 0.003 TYR B 52 PHE 0.027 0.003 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.022 0.004 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00823 / 0.46 (24183) covalent geometry : angle 0.99121 / 0.54 (34337) hydrogen bonds : bond 0.14636 / 9.79 ( 1733) hydrogen bonds : angle 4.98910 / 3.62 ( 4629) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.9488 (mtm) cc_final: 0.9193 (mtp) REVERT: A 121 MET cc_start: 0.8734 (ptp) cc_final: 0.8397 (ptp) REVERT: C 65 GLU cc_start: 0.9118 (tt0) cc_final: 0.8659 (tp30) REVERT: C 100 ARG cc_start: 0.8513 (mmp80) cc_final: 0.8298 (mmm160) REVERT: C 113 GLN cc_start: 0.7840 (tp-100) cc_final: 0.7396 (tp-100) REVERT: D 63 MET cc_start: 0.9709 (mmp) cc_final: 0.9437 (mmm) REVERT: D 100 ARG cc_start: 0.9188 (mmm-85) cc_final: 0.8882 (mmm-85) REVERT: E 55 TYR cc_start: 0.9344 (m-80) cc_final: 0.9008 (m-80) REVERT: E 91 MET cc_start: 0.9373 (mmp) cc_final: 0.9117 (mmm) REVERT: E 105 PHE cc_start: 0.9456 (m-80) cc_final: 0.9052 (m-80) REVERT: E 106 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8520 (tm-30) REVERT: F 88 VAL cc_start: 0.9643 (p) cc_final: 0.9332 (m) REVERT: H 66 PHE cc_start: 0.9602 (t80) cc_final: 0.9359 (t80) REVERT: H 114 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9042 (mm-30) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1221 time to fit residues: 32.8218 Evaluate side-chains 135 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 51 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 243 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 323 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.153786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.107331 restraints weight = 197427.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.107018 restraints weight = 86338.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.107956 restraints weight = 52923.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.107390 restraints weight = 44660.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.107373 restraints weight = 40798.541| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 24183 Z= 0.148 Angle : 0.649 13.420 34337 Z= 0.357 Chirality : 0.045 0.232 4204 Planarity : 0.004 0.043 3714 Dihedral : 25.812 87.835 6163 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.16), residues: 3004 helix: 1.70 (0.12), residues: 1784 sheet: -0.41 (0.42), residues: 169 loop : -0.59 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 117 TYR 0.025 0.002 TYR G 51 PHE 0.019 0.001 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.005 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (24183) covalent geometry : angle 0.64942 / 0.36 (34337) hydrogen bonds : bond 0.04863 / 3.28 ( 1733) hydrogen bonds : angle 3.93575 / 2.84 ( 4629) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.749 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: A 91 MET cc_start: 0.9571 (mtm) cc_final: 0.9231 (mtp) REVERT: A 121 MET cc_start: 0.9106 (ptp) cc_final: 0.8869 (ptp) REVERT: B 68 ARG cc_start: 0.9402 (ttp-110) cc_final: 0.8897 (ttm110) REVERT: B 69 ASP cc_start: 0.9490 (m-30) cc_final: 0.9288 (m-30) REVERT: C 57 GLU cc_start: 0.9179 (tt0) cc_final: 0.8690 (tt0) REVERT: C 100 ARG cc_start: 0.8583 (mmp80) cc_final: 0.8259 (mmm160) REVERT: C 113 GLN cc_start: 0.7490 (tp-100) cc_final: 0.7277 (tp-100) REVERT: D 63 MET cc_start: 0.9656 (mmp) cc_final: 0.9426 (mmm) REVERT: D 71 PHE cc_start: 0.9601 (t80) cc_final: 0.9328 (t80) REVERT: D 90 ILE cc_start: 0.9415 (tp) cc_final: 0.8987 (tp) REVERT: D 107 LEU cc_start: 0.9692 (tp) cc_final: 0.9381 (tp) REVERT: E 51 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8077 (mt-10) REVERT: E 55 TYR cc_start: 0.9257 (m-80) cc_final: 0.9018 (m-80) REVERT: E 91 MET cc_start: 0.9424 (mmp) cc_final: 0.9113 (mmm) REVERT: E 95 GLU cc_start: 0.8791 (tp30) cc_final: 0.8354 (tp30) REVERT: E 101 LEU cc_start: 0.9834 (mm) cc_final: 0.9464 (mm) REVERT: E 104 LEU cc_start: 0.9545 (mm) cc_final: 0.9277 (mm) REVERT: E 105 PHE cc_start: 0.9429 (m-80) cc_final: 0.8874 (m-80) REVERT: E 106 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8412 (tm-30) REVERT: F 61 VAL cc_start: 0.9743 (t) cc_final: 0.9217 (t) REVERT: F 64 GLU cc_start: 0.9348 (mt-10) cc_final: 0.9009 (mt-10) REVERT: G 97 LEU cc_start: 0.9585 (mt) cc_final: 0.9376 (mt) REVERT: H 63 MET cc_start: 0.9772 (mmp) cc_final: 0.9534 (mmm) REVERT: H 66 PHE cc_start: 0.9681 (t80) cc_final: 0.9466 (t80) REVERT: H 101 LEU cc_start: 0.9758 (mt) cc_final: 0.9510 (mt) REVERT: H 114 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9012 (mm-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1311 time to fit residues: 43.7972 Evaluate side-chains 165 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 269 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 chunk 138 optimal weight: 40.0000 chunk 293 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 50.0000 chunk 89 optimal weight: 40.0000 chunk 211 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 208 optimal weight: 50.0000 chunk 232 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.119207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.080017 restraints weight = 99013.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.081717 restraints weight = 54653.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.083218 restraints weight = 36783.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.084299 restraints weight = 26903.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.084952 restraints weight = 21676.751| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 24183 Z= 0.276 Angle : 0.753 17.729 34337 Z= 0.413 Chirality : 0.046 0.252 4204 Planarity : 0.005 0.078 3714 Dihedral : 25.762 88.973 6163 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 3004 helix: 1.48 (0.12), residues: 1801 sheet: -0.47 (0.42), residues: 167 loop : -0.82 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 117 TYR 0.027 0.002 TYR D 84 PHE 0.018 0.001 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.019 0.003 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.28 (24183) covalent geometry : angle 0.75265 / 0.41 (34337) hydrogen bonds : bond 0.08709 / 5.81 ( 1733) hydrogen bonds : angle 4.26575 / 3.09 ( 4629) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8922 (ptp) cc_final: 0.8427 (ptp) REVERT: B 69 ASP cc_start: 0.9536 (m-30) cc_final: 0.9243 (m-30) REVERT: B 85 MET cc_start: 0.9284 (mmt) cc_final: 0.9043 (mmt) REVERT: C 100 ARG cc_start: 0.8403 (mmp80) cc_final: 0.8144 (mmm160) REVERT: C 113 GLN cc_start: 0.7903 (tp-100) cc_final: 0.7417 (tp-100) REVERT: C 115 VAL cc_start: 0.6889 (t) cc_final: 0.6625 (p) REVERT: E 55 TYR cc_start: 0.9253 (m-80) cc_final: 0.8983 (m-80) REVERT: E 91 MET cc_start: 0.9336 (mmp) cc_final: 0.9075 (mmm) REVERT: E 95 GLU cc_start: 0.8722 (tp30) cc_final: 0.8332 (tp30) REVERT: E 104 LEU cc_start: 0.9456 (mm) cc_final: 0.9181 (mm) REVERT: E 105 PHE cc_start: 0.9415 (m-80) cc_final: 0.9008 (m-80) REVERT: E 106 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8365 (tm-30) REVERT: F 64 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8975 (mt-10) REVERT: H 101 LEU cc_start: 0.9833 (mt) cc_final: 0.9609 (mt) REVERT: H 114 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8962 (mm-30) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1352 time to fit residues: 40.0935 Evaluate side-chains 141 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 216 optimal weight: 20.0000 chunk 258 optimal weight: 3.9990 chunk 112 optimal weight: 0.2980 chunk 308 optimal weight: 9.9990 chunk 220 optimal weight: 0.5980 chunk 217 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 287 optimal weight: 0.6980 chunk 157 optimal weight: 0.0470 chunk 194 optimal weight: 0.0470 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.155004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.108924 restraints weight = 196409.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.108318 restraints weight = 85547.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.109466 restraints weight = 51166.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.109362 restraints weight = 42342.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.108954 restraints weight = 38460.781| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 24183 Z= 0.130 Angle : 0.627 10.828 34337 Z= 0.344 Chirality : 0.043 0.204 4204 Planarity : 0.004 0.042 3714 Dihedral : 25.434 86.500 6163 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.16), residues: 3004 helix: 1.97 (0.12), residues: 1811 sheet: -0.22 (0.42), residues: 171 loop : -0.67 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 117 TYR 0.013 0.001 TYR B 89 PHE 0.017 0.001 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 (24183) covalent geometry : angle 0.62704 / 0.34 (34337) hydrogen bonds : bond 0.03884 / 2.57 ( 1733) hydrogen bonds : angle 3.63901 / 2.62 ( 4629) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.9592 (mtm) cc_final: 0.9257 (ptp) REVERT: A 121 MET cc_start: 0.8775 (ptp) cc_final: 0.8315 (ptp) REVERT: B 23 LEU cc_start: 0.6913 (mp) cc_final: 0.6565 (mt) REVERT: B 60 LYS cc_start: 0.9400 (ptpp) cc_final: 0.9072 (ptpp) REVERT: B 64 GLU cc_start: 0.9129 (mp0) cc_final: 0.8823 (pm20) REVERT: B 68 ARG cc_start: 0.9463 (ttp-110) cc_final: 0.8942 (ttm110) REVERT: C 57 GLU cc_start: 0.9180 (tt0) cc_final: 0.8650 (tt0) REVERT: C 65 GLU cc_start: 0.9034 (tt0) cc_final: 0.8704 (tp30) REVERT: C 100 ARG cc_start: 0.8592 (mmp80) cc_final: 0.8223 (mmm160) REVERT: C 113 GLN cc_start: 0.7658 (tp-100) cc_final: 0.7207 (tp-100) REVERT: C 115 VAL cc_start: 0.7328 (t) cc_final: 0.7098 (p) REVERT: E 51 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8197 (mt-10) REVERT: E 55 TYR cc_start: 0.9194 (m-80) cc_final: 0.8949 (m-10) REVERT: E 91 MET cc_start: 0.9471 (mmp) cc_final: 0.9166 (mmm) REVERT: E 95 GLU cc_start: 0.8810 (tp30) cc_final: 0.8294 (tp30) REVERT: E 101 LEU cc_start: 0.9820 (mm) cc_final: 0.9449 (mm) REVERT: E 105 PHE cc_start: 0.9434 (m-80) cc_final: 0.8861 (m-80) REVERT: F 61 VAL cc_start: 0.9730 (t) cc_final: 0.9134 (t) REVERT: F 64 GLU cc_start: 0.9346 (mt-10) cc_final: 0.8940 (mp0) REVERT: H 63 MET cc_start: 0.9721 (mmp) cc_final: 0.9473 (mmm) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1179 time to fit residues: 39.2244 Evaluate side-chains 163 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 163 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 259 optimal weight: 30.0000 chunk 80 optimal weight: 6.9990 chunk 103 optimal weight: 50.0000 chunk 239 optimal weight: 50.0000 chunk 52 optimal weight: 8.9990 chunk 278 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.118526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.079113 restraints weight = 101245.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.081003 restraints weight = 56556.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.082154 restraints weight = 38055.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.083096 restraints weight = 29193.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.083788 restraints weight = 23653.246| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 24183 Z= 0.297 Angle : 0.763 18.190 34337 Z= 0.419 Chirality : 0.047 0.322 4204 Planarity : 0.005 0.071 3714 Dihedral : 25.570 89.952 6163 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 3004 helix: 1.63 (0.12), residues: 1795 sheet: -0.52 (0.44), residues: 158 loop : -0.83 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 41 TYR 0.022 0.002 TYR F 52 PHE 0.019 0.002 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.014 0.003 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.30 (24183) covalent geometry : angle 0.76296 / 0.42 (34337) hydrogen bonds : bond 0.09650 / 6.44 ( 1733) hydrogen bonds : angle 4.29217 / 3.11 ( 4629) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8844 (ptp) cc_final: 0.8448 (ptp) REVERT: B 66 VAL cc_start: 0.9758 (m) cc_final: 0.9555 (m) REVERT: B 69 ASP cc_start: 0.9548 (m-30) cc_final: 0.9235 (m-30) REVERT: B 85 MET cc_start: 0.9377 (mmt) cc_final: 0.9086 (mmt) REVERT: C 65 GLU cc_start: 0.9142 (tt0) cc_final: 0.8791 (tp30) REVERT: C 113 GLN cc_start: 0.7538 (tp-100) cc_final: 0.7085 (tp-100) REVERT: C 115 VAL cc_start: 0.7126 (t) cc_final: 0.6902 (p) REVERT: D 72 GLU cc_start: 0.9228 (mp0) cc_final: 0.8996 (mp0) REVERT: E 55 TYR cc_start: 0.9273 (m-80) cc_final: 0.8982 (m-80) REVERT: E 91 MET cc_start: 0.9397 (mmp) cc_final: 0.9157 (mmm) REVERT: E 95 GLU cc_start: 0.8828 (tp30) cc_final: 0.8397 (tp30) REVERT: E 101 LEU cc_start: 0.9832 (mm) cc_final: 0.9585 (mm) REVERT: E 105 PHE cc_start: 0.9488 (m-80) cc_final: 0.9067 (m-80) REVERT: F 64 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9028 (mt-10) REVERT: F 71 VAL cc_start: 0.9854 (m) cc_final: 0.9551 (p) REVERT: H 66 PHE cc_start: 0.9531 (t80) cc_final: 0.9330 (t80) REVERT: H 114 GLU cc_start: 0.8775 (mp0) cc_final: 0.8485 (mp0) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1207 time to fit residues: 36.1099 Evaluate side-chains 144 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 324 optimal weight: 20.0000 chunk 88 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 chunk 206 optimal weight: 50.0000 chunk 145 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 180 optimal weight: 0.0270 chunk 222 optimal weight: 40.0000 chunk 36 optimal weight: 1.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.153474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.107898 restraints weight = 196220.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.107196 restraints weight = 89544.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.108942 restraints weight = 57707.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.108305 restraints weight = 54222.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.107739 restraints weight = 48519.060| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 24183 Z= 0.132 Angle : 0.617 12.729 34337 Z= 0.342 Chirality : 0.043 0.202 4204 Planarity : 0.004 0.045 3714 Dihedral : 25.446 85.358 6163 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.16), residues: 3004 helix: 2.01 (0.12), residues: 1809 sheet: -0.21 (0.44), residues: 165 loop : -0.73 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 43 TYR 0.014 0.001 TYR E 42 PHE 0.014 0.001 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.008 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (24183) covalent geometry : angle 0.61738 / 0.34 (34337) hydrogen bonds : bond 0.04044 / 2.69 ( 1733) hydrogen bonds : angle 3.71245 / 2.67 ( 4629) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6026.28 seconds wall clock time: 103 minutes 8.41 seconds (6188.41 seconds total)