Starting phenix.real_space_refine on Sat Jul 4 22:17:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rn2_54078/07_2026/9rn2_54078.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rn2_54078/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9rn2_54078/07_2026/9rn2_54078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rn2_54078/07_2026/9rn2_54078.map" model { file = "/net/cci-nas-00/data/ceres_data/9rn2_54078/07_2026/9rn2_54078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rn2_54078/07_2026/9rn2_54078.cif" } 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-dev-6108/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: 4.44, per 1000 atoms: 0.19 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: 1.71 Conformation dependent library (CDL) restraints added in 966.1 milliseconds 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: 2.96 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: 8.01 Time building geometry restraints manager: 2.22 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: 31647 2.07 - 4.14: 2101 4.14 - 6.20: 458 6.20 - 8.27: 124 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: 0.900 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.710 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.090 ------------------------------------------------------------------------------- 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= 0.806 Angle : 1.214 10.339 34337 Z= 0.792 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 1.21372 / 0.79 (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 : 0.696 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: 0.8532 (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: 0.8721 (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: 0.9140 (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: 0.1254 time to fit residues: 60.0697 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 : 0.700 ------------------------------------------------------------------------------- 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 85 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS E 69 GLN F 94 GLN H 83 HIS H 110 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.120861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.082162 restraints weight = 98765.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.084258 restraints weight = 52763.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.085536 restraints weight = 34487.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.086657 restraints weight = 25630.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.087462 restraints weight = 20552.846| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.153 24183 Z= 0.411 Angle : 1.000 14.722 34337 Z= 0.535 Chirality : 0.053 0.294 4204 Planarity : 0.007 0.113 3714 Dihedral : 26.490 77.373 6163 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: 0.32 (0.15), residues: 3004 helix: 0.76 (0.12), residues: 1795 sheet: -0.28 (0.43), residues: 160 loop : -0.53 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.057 0.002 ARG D 80 TYR 0.025 0.003 TYR D 84 PHE 0.019 0.002 PHE F 101 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 0.00734 / 0.41 (24183) covalent geometry : angle 1.00016 / 0.54 (34337) hydrogen bonds : bond 0.11504 / 7.78 ( 1733) hydrogen bonds : angle 4.98020 / 3.58 ( 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 197 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.551 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: 0.9306 (mt-10) cc_final: 0.8976 (mt-10) REVERT: A 56 GLN cc_start: 0.8961 (mt0) cc_final: 0.8745 (mt0) REVERT: A 91 MET cc_start: 0.9441 (mtm) cc_final: 0.9153 (mtp) REVERT: A 106 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8448 (tm-30) REVERT: B 60 LYS cc_start: 0.9616 (tttt) cc_final: 0.9109 (ptmm) REVERT: B 69 ASP cc_start: 0.9582 (m-30) cc_final: 0.9334 (m-30) REVERT: B 94 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8814 (tm-30) REVERT: C 57 GLU cc_start: 0.9077 (tt0) cc_final: 0.8495 (mt-10) REVERT: C 65 GLU cc_start: 0.9597 (tt0) cc_final: 0.9218 (tm-30) REVERT: D 63 MET cc_start: 0.9572 (mmm) cc_final: 0.9363 (mmm) REVERT: D 70 ILE cc_start: 0.9693 (mm) cc_final: 0.9422 (mm) REVERT: E 51 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8486 (mt-10) REVERT: F 64 GLU cc_start: 0.9513 (mt-10) cc_final: 0.9220 (mt-10) REVERT: F 69 ASP cc_start: 0.9271 (m-30) cc_final: 0.8991 (t0) REVERT: G 91 ASP cc_start: 0.9201 (t0) cc_final: 0.8615 (t0) REVERT: G 94 LEU cc_start: 0.9706 (mt) cc_final: 0.9348 (mt) REVERT: H 66 PHE cc_start: 0.9592 (t80) cc_final: 0.9282 (t80) REVERT: H 114 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9113 (mm-30) outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.1162 time to fit residues: 37.9579 Evaluate side-chains 161 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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: 8.9990 chunk 293 optimal weight: 30.0000 chunk 252 optimal weight: 50.0000 chunk 260 optimal weight: 30.0000 chunk 177 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 220 optimal weight: 40.0000 chunk 180 optimal weight: 0.1980 chunk 143 optimal weight: 0.0030 chunk 41 optimal weight: 1.9990 chunk 162 optimal weight: 50.0000 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.127677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.086074 restraints weight = 97835.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.088278 restraints weight = 50595.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.089760 restraints weight = 32263.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.090872 restraints weight = 23305.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.091657 restraints weight = 18498.621| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24183 Z= 0.163 Angle : 0.634 9.666 34337 Z= 0.356 Chirality : 0.043 0.213 4204 Planarity : 0.004 0.051 3714 Dihedral : 25.927 87.071 6163 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.28 % Allowed : 2.75 % Favored : 96.97 % 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: -0.24 (0.42), residues: 165 loop : -0.35 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 80 TYR 0.015 0.001 TYR D 43 PHE 0.027 0.001 PHE D 71 TRP 0.000 0.000 TRP I 764 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.16 (24183) covalent geometry : angle 0.63446 / 0.36 (34337) hydrogen bonds : bond 0.04937 / 3.28 ( 1733) hydrogen bonds : angle 3.96568 / 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 215 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 0.525 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: A 56 GLN cc_start: 0.8882 (mt0) cc_final: 0.8171 (tt0) REVERT: A 91 MET cc_start: 0.9497 (mtm) cc_final: 0.9140 (mtp) REVERT: A 105 PHE cc_start: 0.9613 (m-80) cc_final: 0.9130 (m-10) REVERT: A 106 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8356 (tm-30) REVERT: A 110 LEU cc_start: 0.9523 (mt) cc_final: 0.9295 (mt) REVERT: A 121 MET cc_start: 0.8640 (ptp) cc_final: 0.8263 (ptp) REVERT: B 60 LYS cc_start: 0.9501 (tttt) cc_final: 0.9205 (ptpp) REVERT: B 69 ASP cc_start: 0.9434 (m-30) cc_final: 0.9160 (m-30) REVERT: B 94 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8859 (tm-30) REVERT: C 57 GLU cc_start: 0.9122 (tt0) cc_final: 0.8532 (tt0) REVERT: C 65 GLU cc_start: 0.9589 (tt0) cc_final: 0.9161 (tm-30) REVERT: D 63 MET cc_start: 0.9629 (mmm) cc_final: 0.9402 (mmm) REVERT: D 90 ILE cc_start: 0.9611 (tp) cc_final: 0.9345 (tp) REVERT: E 51 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8269 (mt-10) REVERT: E 55 TYR cc_start: 0.9298 (m-80) cc_final: 0.9043 (m-80) REVERT: E 91 MET cc_start: 0.9508 (mmp) cc_final: 0.9243 (mmm) REVERT: E 95 GLU cc_start: 0.8748 (tp30) cc_final: 0.8487 (tp30) REVERT: E 104 LEU cc_start: 0.9586 (mm) cc_final: 0.9256 (mm) REVERT: E 105 PHE cc_start: 0.9551 (m-10) cc_final: 0.9240 (m-10) REVERT: F 61 VAL cc_start: 0.9876 (t) cc_final: 0.9403 (t) REVERT: F 64 GLU cc_start: 0.9455 (mt-10) cc_final: 0.9017 (mt-10) REVERT: F 69 ASP cc_start: 0.9182 (m-30) cc_final: 0.8759 (t0) REVERT: G 91 ASP cc_start: 0.9097 (t0) cc_final: 0.8594 (t0) REVERT: H 66 PHE cc_start: 0.9531 (t80) cc_final: 0.9187 (t80) REVERT: H 107 LEU cc_start: 0.9688 (mt) cc_final: 0.9433 (mt) REVERT: H 114 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9112 (mm-30) outliers start: 2 outliers final: 1 residues processed: 213 average time/residue: 0.1153 time to fit residues: 41.6757 Evaluate side-chains 178 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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: 40.0000 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 40.0000 chunk 186 optimal weight: 8.9990 chunk 122 optimal weight: 40.0000 chunk 316 optimal weight: 30.0000 chunk 168 optimal weight: 5.9990 chunk 320 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 293 optimal weight: 7.9990 chunk 235 optimal weight: 30.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.121313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.081494 restraints weight = 98184.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.083453 restraints weight = 53466.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.084842 restraints weight = 35155.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.085720 restraints weight = 26088.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.086494 restraints weight = 21241.847| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 24183 Z= 0.291 Angle : 0.772 16.753 34337 Z= 0.424 Chirality : 0.046 0.249 4204 Planarity : 0.005 0.050 3714 Dihedral : 25.841 84.768 6163 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.14 % Allowed : 4.68 % Favored : 95.18 % 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: 0.95 (0.15), residues: 3004 helix: 1.42 (0.12), residues: 1793 sheet: -0.15 (0.43), residues: 157 loop : -0.54 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 73 TYR 0.025 0.002 TYR F 52 PHE 0.022 0.002 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.012 0.003 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.29 (24183) covalent geometry : angle 0.77187 / 0.42 (34337) hydrogen bonds : bond 0.09736 / 6.49 ( 1733) hydrogen bonds : angle 4.29099 / 3.11 ( 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 183 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9274 (mt-10) cc_final: 0.9040 (tt0) REVERT: A 91 MET cc_start: 0.9423 (mtm) cc_final: 0.9172 (mtp) REVERT: A 106 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 110 LEU cc_start: 0.9248 (mt) cc_final: 0.8879 (mt) REVERT: A 121 MET cc_start: 0.8632 (ptp) cc_final: 0.7856 (ptp) REVERT: B 60 LYS cc_start: 0.9451 (tttt) cc_final: 0.9208 (ptmm) REVERT: B 64 GLU cc_start: 0.9161 (mp0) cc_final: 0.8890 (mp0) REVERT: B 69 ASP cc_start: 0.9393 (m-30) cc_final: 0.9071 (m-30) REVERT: C 65 GLU cc_start: 0.9369 (tt0) cc_final: 0.8993 (tp30) REVERT: D 63 MET cc_start: 0.9616 (mmm) cc_final: 0.9400 (mmm) REVERT: D 114 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8319 (tm-30) REVERT: E 51 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8551 (mt-10) REVERT: E 91 MET cc_start: 0.9380 (mmp) cc_final: 0.9121 (mmm) REVERT: E 95 GLU cc_start: 0.8709 (tp30) cc_final: 0.8463 (tp30) REVERT: E 104 LEU cc_start: 0.9528 (mm) cc_final: 0.9181 (mm) REVERT: F 51 ILE cc_start: 0.9017 (mm) cc_final: 0.8816 (mm) REVERT: F 64 GLU cc_start: 0.9412 (mt-10) cc_final: 0.8933 (mt-10) REVERT: H 46 LEU cc_start: 0.9622 (pp) cc_final: 0.9314 (tp) REVERT: H 66 PHE cc_start: 0.9533 (t80) cc_final: 0.9303 (t80) REVERT: H 114 GLU cc_start: 0.9350 (mm-30) cc_final: 0.8990 (mm-30) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1160 time to fit residues: 36.2783 Evaluate side-chains 150 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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: 0.9990 chunk 42 optimal weight: 0.8980 chunk 249 optimal weight: 40.0000 chunk 271 optimal weight: 40.0000 chunk 313 optimal weight: 30.0000 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 86 optimal weight: 50.0000 chunk 31 optimal weight: 0.9990 chunk 234 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.156029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.117181 restraints weight = 194268.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.113382 restraints weight = 108260.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.113672 restraints weight = 70122.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.112952 restraints weight = 54950.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.113213 restraints weight = 54414.041| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 24183 Z= 0.130 Angle : 0.600 8.117 34337 Z= 0.336 Chirality : 0.043 0.212 4204 Planarity : 0.004 0.046 3714 Dihedral : 25.584 84.880 6163 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: 1.59 (0.15), residues: 3004 helix: 2.03 (0.12), residues: 1781 sheet: -0.31 (0.41), residues: 176 loop : -0.38 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 117 TYR 0.018 0.002 TYR B 52 PHE 0.012 0.001 PHE B 62 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 0.00232 / 0.13 (24183) covalent geometry : angle 0.59981 / 0.34 (34337) hydrogen bonds : bond 0.04091 / 2.71 ( 1733) hydrogen bonds : angle 3.71206 / 2.68 ( 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 208 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.560 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: A 51 GLU cc_start: 0.9503 (mt-10) cc_final: 0.9123 (mt-10) REVERT: A 91 MET cc_start: 0.9593 (mtm) cc_final: 0.9258 (mtp) REVERT: A 121 MET cc_start: 0.8766 (ptp) cc_final: 0.8302 (mtp) REVERT: B 64 GLU cc_start: 0.9269 (mp0) cc_final: 0.8830 (mp0) REVERT: B 68 ARG cc_start: 0.9422 (ttp-110) cc_final: 0.8913 (ttm110) REVERT: B 94 GLN cc_start: 0.9304 (tm-30) cc_final: 0.8916 (tm-30) REVERT: C 57 GLU cc_start: 0.9140 (tt0) cc_final: 0.8604 (tt0) REVERT: C 65 GLU cc_start: 0.9315 (tt0) cc_final: 0.9090 (tm-30) REVERT: C 115 VAL cc_start: 0.7189 (t) cc_final: 0.6673 (t) REVERT: D 63 MET cc_start: 0.9557 (mmm) cc_final: 0.9229 (mmp) REVERT: D 90 ILE cc_start: 0.9535 (tp) cc_final: 0.9323 (tp) REVERT: D 114 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8343 (tm-30) REVERT: E 42 TYR cc_start: 0.5905 (m-80) cc_final: 0.5616 (m-80) REVERT: E 51 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8253 (mt-10) REVERT: E 55 TYR cc_start: 0.9387 (m-80) cc_final: 0.9082 (m-80) REVERT: E 91 MET cc_start: 0.9476 (mmp) cc_final: 0.9171 (mmm) REVERT: E 95 GLU cc_start: 0.8841 (tp30) cc_final: 0.8437 (tp30) REVERT: E 101 LEU cc_start: 0.9847 (mm) cc_final: 0.9526 (mm) REVERT: E 104 LEU cc_start: 0.9603 (mm) cc_final: 0.9339 (mm) REVERT: E 105 PHE cc_start: 0.9528 (m-10) cc_final: 0.9116 (m-80) REVERT: F 61 VAL cc_start: 0.9740 (t) cc_final: 0.9180 (t) REVERT: F 64 GLU cc_start: 0.9372 (mt-10) cc_final: 0.8945 (mt-10) REVERT: G 91 ASP cc_start: 0.8694 (t0) cc_final: 0.8164 (t0) REVERT: H 66 PHE cc_start: 0.9635 (t80) cc_final: 0.9367 (t80) REVERT: H 114 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9110 (mm-30) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1213 time to fit residues: 42.8105 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 : 0.708 ------------------------------------------------------------------------------- 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: 10.0000 chunk 227 optimal weight: 40.0000 chunk 144 optimal weight: 0.8980 chunk 242 optimal weight: 50.0000 chunk 55 optimal weight: 9.9990 chunk 124 optimal weight: 50.0000 chunk 169 optimal weight: 50.0000 chunk 196 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 118 optimal weight: 40.0000 overall best weight: 9.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4412 r_free = 0.4412 target = 0.116477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.077855 restraints weight = 102905.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.079477 restraints weight = 57834.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.080879 restraints weight = 39885.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.081864 restraints weight = 29025.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.082441 restraints weight = 23538.167| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 24183 Z= 0.417 Angle : 0.898 19.730 34337 Z= 0.496 Chirality : 0.050 0.316 4204 Planarity : 0.006 0.074 3714 Dihedral : 26.016 87.630 6163 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.14 % Allowed : 3.17 % Favored : 96.69 % 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: 0.40 (0.15), residues: 3004 helix: 0.99 (0.12), residues: 1794 sheet: -0.39 (0.43), residues: 154 loop : -0.80 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 41 TYR 0.034 0.003 TYR F 52 PHE 0.023 0.002 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.017 0.003 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00741 / 0.42 (24183) covalent geometry : angle 0.89804 / 0.50 (34337) hydrogen bonds : bond 0.12611 / 8.43 ( 1733) hydrogen bonds : angle 4.82902 / 3.51 ( 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 157 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.605 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: 0.9471 (mtm) cc_final: 0.9175 (mtp) REVERT: A 110 LEU cc_start: 0.9516 (mt) cc_final: 0.8702 (mt) REVERT: A 121 MET cc_start: 0.8771 (ptp) cc_final: 0.8294 (ptp) REVERT: C 65 GLU cc_start: 0.9114 (tt0) cc_final: 0.8658 (tp30) REVERT: C 113 GLN cc_start: 0.7836 (tp-100) cc_final: 0.7410 (tp-100) REVERT: D 63 MET cc_start: 0.9660 (mmm) cc_final: 0.9406 (mmm) REVERT: D 100 ARG cc_start: 0.9229 (mmm-85) cc_final: 0.8924 (mmm-85) REVERT: D 114 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8397 (tm-30) REVERT: E 91 MET cc_start: 0.9431 (mmp) cc_final: 0.9177 (mmm) REVERT: E 95 GLU cc_start: 0.8856 (tp30) cc_final: 0.8615 (tp30) REVERT: H 66 PHE cc_start: 0.9625 (t80) cc_final: 0.9402 (t80) REVERT: H 114 GLU cc_start: 0.9276 (mm-30) cc_final: 0.9060 (mm-30) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.1163 time to fit residues: 31.0233 Evaluate side-chains 132 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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: 3.9990 chunk 197 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 323 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 225 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.153005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.105987 restraints weight = 197415.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.105643 restraints weight = 88274.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.106474 restraints weight = 58561.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.106391 restraints weight = 45801.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.106348 restraints weight = 41329.478| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 24183 Z= 0.162 Angle : 0.635 13.791 34337 Z= 0.356 Chirality : 0.044 0.224 4204 Planarity : 0.004 0.044 3714 Dihedral : 25.885 89.982 6163 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: 1.08 (0.16), residues: 3004 helix: 1.65 (0.12), residues: 1795 sheet: -0.43 (0.41), residues: 170 loop : -0.68 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 117 TYR 0.025 0.002 TYR B 89 PHE 0.015 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 0.00299 / 0.16 (24183) covalent geometry : angle 0.63507 / 0.36 (34337) hydrogen bonds : bond 0.05040 / 3.40 ( 1733) hydrogen bonds : angle 3.99031 / 2.88 ( 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 190 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.699 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: A 91 MET cc_start: 0.9611 (mtm) cc_final: 0.9259 (mtp) REVERT: A 121 MET cc_start: 0.8765 (ptp) cc_final: 0.8266 (ptp) REVERT: B 69 ASP cc_start: 0.9516 (m-30) cc_final: 0.9306 (m-30) REVERT: B 85 MET cc_start: 0.9185 (mmt) cc_final: 0.8981 (mmt) REVERT: C 52 LEU cc_start: 0.9727 (mm) cc_final: 0.9512 (mm) REVERT: C 100 ARG cc_start: 0.8686 (mmp80) cc_final: 0.8412 (mmm160) REVERT: C 113 GLN cc_start: 0.7516 (tp-100) cc_final: 0.7218 (tp-100) REVERT: D 63 MET cc_start: 0.9634 (mmm) cc_final: 0.9368 (mmm) REVERT: D 100 ARG cc_start: 0.9330 (mmm-85) cc_final: 0.8960 (mmm-85) REVERT: D 107 LEU cc_start: 0.9786 (tp) cc_final: 0.9501 (mt) REVERT: D 114 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8283 (tm-30) REVERT: E 51 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8215 (mt-10) REVERT: E 91 MET cc_start: 0.9423 (mmp) cc_final: 0.9133 (mmm) REVERT: E 95 GLU cc_start: 0.8786 (tp30) cc_final: 0.8398 (tp30) REVERT: E 101 LEU cc_start: 0.9837 (mm) cc_final: 0.9529 (mm) REVERT: E 104 LEU cc_start: 0.9573 (mm) cc_final: 0.9331 (mm) REVERT: E 105 PHE cc_start: 0.9519 (m-10) cc_final: 0.9151 (m-80) REVERT: F 61 VAL cc_start: 0.9731 (t) cc_final: 0.9218 (t) REVERT: F 64 GLU cc_start: 0.9351 (mt-10) cc_final: 0.9042 (mt-10) REVERT: H 63 MET cc_start: 0.9807 (mmp) cc_final: 0.9570 (mmm) REVERT: H 66 PHE cc_start: 0.9727 (t80) cc_final: 0.9519 (t80) REVERT: H 114 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8939 (mm-30) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1108 time to fit residues: 36.2095 Evaluate side-chains 158 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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: 50.0000 chunk 190 optimal weight: 5.9990 chunk 138 optimal weight: 30.0000 chunk 293 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 50.0000 chunk 89 optimal weight: 30.0000 chunk 211 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 232 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.122524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.082386 restraints weight = 96700.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.084325 restraints weight = 52795.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.085768 restraints weight = 34668.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.086603 restraints weight = 25681.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.087379 restraints weight = 21036.615| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 24183 Z= 0.197 Angle : 0.646 14.438 34337 Z= 0.361 Chirality : 0.043 0.239 4204 Planarity : 0.004 0.043 3714 Dihedral : 25.656 89.354 6163 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: 1.24 (0.16), residues: 3004 helix: 1.82 (0.12), residues: 1800 sheet: -0.37 (0.42), residues: 168 loop : -0.74 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 93 TYR 0.019 0.002 TYR F 89 PHE 0.013 0.001 PHE C 26 TRP 0.000 0.000 TRP I 764 HIS 0.007 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.20 (24183) covalent geometry : angle 0.64616 / 0.36 (34337) hydrogen bonds : bond 0.06241 / 4.14 ( 1733) hydrogen bonds : angle 3.93245 / 2.84 ( 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 180 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.664 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: B 69 ASP cc_start: 0.9490 (m-30) cc_final: 0.9253 (m-30) REVERT: B 85 MET cc_start: 0.9320 (mmt) cc_final: 0.9073 (mmt) REVERT: C 100 ARG cc_start: 0.8273 (mmp80) cc_final: 0.8057 (mmm160) REVERT: C 113 GLN cc_start: 0.7532 (tp-100) cc_final: 0.7139 (tp-100) REVERT: C 115 VAL cc_start: 0.6875 (t) cc_final: 0.6640 (p) REVERT: D 100 ARG cc_start: 0.9170 (mmm-85) cc_final: 0.8750 (mmm-85) REVERT: D 114 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8262 (tm-30) REVERT: E 51 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8196 (mt-10) REVERT: E 91 MET cc_start: 0.9340 (mmp) cc_final: 0.9067 (mmm) REVERT: E 95 GLU cc_start: 0.8677 (tp30) cc_final: 0.8319 (tt0) REVERT: E 101 LEU cc_start: 0.9840 (mm) cc_final: 0.9499 (mm) REVERT: E 105 PHE cc_start: 0.9482 (m-10) cc_final: 0.9162 (m-80) REVERT: F 61 VAL cc_start: 0.9774 (t) cc_final: 0.9338 (t) REVERT: F 64 GLU cc_start: 0.9365 (mt-10) cc_final: 0.8938 (mt-10) REVERT: G 113 GLN cc_start: 0.8233 (tp40) cc_final: 0.7776 (tp40) REVERT: H 66 PHE cc_start: 0.9501 (t80) cc_final: 0.9294 (t80) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1283 time to fit residues: 39.5179 Evaluate side-chains 149 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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: 9.9990 chunk 258 optimal weight: 0.0370 chunk 112 optimal weight: 50.0000 chunk 308 optimal weight: 10.0000 chunk 220 optimal weight: 0.0870 chunk 217 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 287 optimal weight: 30.0000 chunk 157 optimal weight: 0.0030 chunk 194 optimal weight: 30.0000 overall best weight: 3.8250 ------------------------------------------------------------------------------- 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** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.151537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.105614 restraints weight = 197722.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.104451 restraints weight = 102974.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.104974 restraints weight = 63762.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.104660 restraints weight = 45560.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.104678 restraints weight = 37361.606| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 : 0.004 0.106 24183 Z= 0.201 Angle : 0.636 14.337 34337 Z= 0.359 Chirality : 0.043 0.230 4204 Planarity : 0.005 0.056 3714 Dihedral : 25.621 90.278 6163 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: 1.23 (0.16), residues: 3004 helix: 1.85 (0.12), residues: 1801 sheet: -0.31 (0.45), residues: 154 loop : -0.84 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 117 TYR 0.031 0.002 TYR D 84 PHE 0.015 0.001 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.011 0.002 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.20 (24183) covalent geometry : angle 0.63640 / 0.36 (34337) hydrogen bonds : bond 0.05595 / 3.78 ( 1733) hydrogen bonds : angle 3.93496 / 2.84 ( 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 176 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.681 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: 0.9570 (mtm) cc_final: 0.9345 (mtp) REVERT: A 121 MET cc_start: 0.8839 (ptp) cc_final: 0.8591 (ptp) REVERT: B 64 GLU cc_start: 0.9110 (mp0) cc_final: 0.8888 (mp0) REVERT: B 69 ASP cc_start: 0.9520 (m-30) cc_final: 0.9154 (m-30) REVERT: B 85 MET cc_start: 0.9447 (mmt) cc_final: 0.9178 (mmt) REVERT: C 100 ARG cc_start: 0.8607 (mmp80) cc_final: 0.8375 (mmm160) REVERT: C 113 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7296 (tp-100) REVERT: C 115 VAL cc_start: 0.7128 (t) cc_final: 0.6904 (p) REVERT: D 63 MET cc_start: 0.9649 (mmp) cc_final: 0.9439 (mmm) REVERT: D 100 ARG cc_start: 0.9342 (mmm-85) cc_final: 0.9045 (mmm-85) REVERT: D 114 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8203 (tm-30) REVERT: E 91 MET cc_start: 0.9426 (mmp) cc_final: 0.9144 (mmm) REVERT: E 95 GLU cc_start: 0.8780 (tp30) cc_final: 0.8329 (tt0) REVERT: E 101 LEU cc_start: 0.9853 (mm) cc_final: 0.9502 (mm) REVERT: E 105 PHE cc_start: 0.9468 (m-10) cc_final: 0.9146 (m-80) REVERT: F 61 VAL cc_start: 0.9731 (t) cc_final: 0.9233 (t) REVERT: F 64 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8846 (mt-10) REVERT: F 85 MET cc_start: 0.8857 (tpt) cc_final: 0.8614 (tpp) REVERT: H 63 MET cc_start: 0.9782 (mmp) cc_final: 0.9557 (mmm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1272 time to fit residues: 37.9154 Evaluate side-chains 152 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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: 0.7980 chunk 48 optimal weight: 0.3980 chunk 322 optimal weight: 10.0000 chunk 259 optimal weight: 50.0000 chunk 80 optimal weight: 5.9990 chunk 103 optimal weight: 40.0000 chunk 239 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 278 optimal weight: 6.9990 chunk 293 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.153741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.108482 restraints weight = 197001.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.107701 restraints weight = 92961.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.107823 restraints weight = 51260.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.108095 restraints weight = 39750.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.109437 restraints weight = 36955.745| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 24183 Z= 0.129 Angle : 0.594 12.204 34337 Z= 0.332 Chirality : 0.042 0.201 4204 Planarity : 0.004 0.048 3714 Dihedral : 25.359 86.809 6163 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.14 % Allowed : 0.69 % Favored : 99.17 % 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: 1.56 (0.16), residues: 3004 helix: 2.13 (0.12), residues: 1803 sheet: -0.21 (0.44), residues: 166 loop : -0.74 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 117 TYR 0.017 0.001 TYR D 84 PHE 0.014 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 0.00228 / 0.13 (24183) covalent geometry : angle 0.59370 / 0.33 (34337) hydrogen bonds : bond 0.03812 / 2.51 ( 1733) hydrogen bonds : angle 3.59711 / 2.59 ( 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 189 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.9090 (t70) cc_final: 0.8799 (t70) REVERT: A 91 MET cc_start: 0.9599 (mtm) cc_final: 0.9285 (mtp) REVERT: A 121 MET cc_start: 0.8743 (ptp) cc_final: 0.8181 (ptp) REVERT: B 64 GLU cc_start: 0.9184 (mp0) cc_final: 0.8876 (pm20) REVERT: B 68 ARG cc_start: 0.9384 (ttp-110) cc_final: 0.9045 (ttm110) REVERT: B 69 ASP cc_start: 0.9431 (m-30) cc_final: 0.9144 (m-30) REVERT: B 85 MET cc_start: 0.9355 (mmt) cc_final: 0.9116 (mmt) REVERT: C 57 GLU cc_start: 0.9012 (tt0) cc_final: 0.8383 (tt0) REVERT: C 65 GLU cc_start: 0.9050 (tt0) cc_final: 0.8718 (tp30) REVERT: C 100 ARG cc_start: 0.8596 (mmp80) cc_final: 0.8367 (mmm160) REVERT: C 113 GLN cc_start: 0.7709 (tp-100) cc_final: 0.7410 (tp-100) REVERT: C 115 VAL cc_start: 0.7160 (t) cc_final: 0.6898 (p) REVERT: D 63 MET cc_start: 0.9645 (mmp) cc_final: 0.9438 (mmm) REVERT: D 100 ARG cc_start: 0.9288 (mmm-85) cc_final: 0.8835 (mmm-85) REVERT: E 51 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8080 (mt-10) REVERT: E 91 MET cc_start: 0.9394 (mmp) cc_final: 0.9102 (mmm) REVERT: E 95 GLU cc_start: 0.8616 (tp30) cc_final: 0.8210 (tp30) REVERT: E 101 LEU cc_start: 0.9820 (mm) cc_final: 0.9475 (mm) REVERT: E 105 PHE cc_start: 0.9341 (m-10) cc_final: 0.9011 (m-80) REVERT: F 61 VAL cc_start: 0.9695 (t) cc_final: 0.9042 (t) REVERT: F 64 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8975 (mp0) REVERT: G 91 ASP cc_start: 0.8849 (t0) cc_final: 0.8480 (t0) REVERT: H 63 MET cc_start: 0.9829 (mmp) cc_final: 0.9583 (mmm) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.1157 time to fit residues: 37.5986 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 : 0.782 ------------------------------------------------------------------------------- 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: 0.6980 chunk 102 optimal weight: 0.9990 chunk 206 optimal weight: 20.0000 chunk 145 optimal weight: 0.0670 chunk 233 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 180 optimal weight: 0.0050 chunk 222 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.7536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 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 = 0.4594 r_free = 0.4594 target = 0.154117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.108917 restraints weight = 195875.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.108310 restraints weight = 89313.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.108357 restraints weight = 60501.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.108746 restraints weight = 51764.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.108796 restraints weight = 39639.222| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 24183 Z= 0.126 Angle : 0.589 11.725 34337 Z= 0.329 Chirality : 0.042 0.208 4204 Planarity : 0.004 0.041 3714 Dihedral : 25.175 86.118 6163 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: 1.69 (0.16), residues: 3004 helix: 2.22 (0.12), residues: 1808 sheet: -0.09 (0.44), residues: 165 loop : -0.67 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 100 TYR 0.026 0.001 TYR B 89 PHE 0.013 0.001 PHE E 68 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 0.00228 / 0.13 (24183) covalent geometry : angle 0.58894 / 0.33 (34337) hydrogen bonds : bond 0.03689 / 2.43 ( 1733) hydrogen bonds : angle 3.52493 / 2.53 ( 4629) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5401.80 seconds wall clock time: 92 minutes 30.14 seconds (5550.14 seconds total)